PLUMED-NEST

Project ID: plumID:19.081
Source: Na/03_MultithermalMultibaric/Reweight/plumed.dat
Originally used with PLUMED version: 2.6-dev
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

Click on the labels of the actions for more information on what each action computes

# vim:ft=plumed
Enables syntax highlighting for PLUMED files in vim. See here for more details. 

energyThe READ action with label energy calculates the following quantities:
 Quantity   
 Type   
 Description  
energy
scalar
the value calculated by this action: 
READ
Read quantities from a colvar file. This action has hidden defaults. More details
 
FILE
the name of the file from which to read these quantities
=COLVARtrim 
VALUES
the values to read from the file
=energy  
IGNORE_TIME
 ignore the time in the colvar file
energy: 
READ
Read quantities from a colvar file. This action uses the defaults shown here. More details
 
FILE
the name of the file from which to read these quantities
=COLVARtrim 
VALUES
the values to read from the file
=energy  
IGNORE_TIME
 ignore the time in the colvar file
  
STRIDE
 the frequency with which the file should be read
=1 
EVERY
 only read every nth line of the colvar file
=1
b1The READ action with label b1 calculates the following quantities:
 Quantity   
 Type   
 Description  
b1.bias
scalar
values from the column labelled b1.bias in the file named COLVARtrim: 
READ
Read quantities from a colvar file. This action has hidden defaults. More details
 
FILE
the name of the file from which to read these quantities
=COLVARtrim 
VALUES
the values to read from the file
=b1.bias  
IGNORE_TIME
 ignore the time in the colvar file
b1: 
READ
Read quantities from a colvar file. This action uses the defaults shown here. More details
 
FILE
the name of the file from which to read these quantities
=COLVARtrim 
VALUES
the values to read from the file
=b1.bias  
IGNORE_TIME
 ignore the time in the colvar file
  
STRIDE
 the frequency with which the file should be read
=1 
EVERY
 only read every nth line of the colvar file
=1
uwallThe READ action with label uwall calculates the following quantities:
 Quantity   
 Type   
 Description  
uwall.bias
scalar
values from the column labelled uwall.bias in the file named COLVARtrim: 
READ
Read quantities from a colvar file. This action has hidden defaults. More details
 
FILE
the name of the file from which to read these quantities
=COLVARtrim 
VALUES
the values to read from the file
=uwall.bias 
IGNORE_TIME
 ignore the time in the colvar file
uwall: 
READ
Read quantities from a colvar file. This action uses the defaults shown here. More details
 
FILE
the name of the file from which to read these quantities
=COLVARtrim 
VALUES
the values to read from the file
=uwall.bias 
IGNORE_TIME
 ignore the time in the colvar file
  
STRIDE
 the frequency with which the file should be read
=1 
EVERY
 only read every nth line of the colvar file
=1
refcvThe READ action with label refcv calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv.morethan
scalar
values from the column labelled refcv.morethan in the file named COLVARtrim: 
READ
Read quantities from a colvar file. This action has hidden defaults. More details
 
FILE
the name of the file from which to read these quantities
=COLVARtrim 
VALUES
the values to read from the file
=refcv.morethan  
IGNORE_TIME
 ignore the time in the colvar file
refcv: 
READ
Read quantities from a colvar file. This action uses the defaults shown here. More details
 
FILE
the name of the file from which to read these quantities
=COLVARtrim 
VALUES
the values to read from the file
=refcv.morethan  
IGNORE_TIME
 ignore the time in the colvar file
  
STRIDE
 the frequency with which the file should be read
=1 
EVERY
 only read every nth line of the colvar file
=1
voltmpThe READ action with label voltmp calculates the following quantities:
 Quantity   
 Type   
 Description  
voltmp
scalar
the value calculated by this action: 
READ
Read quantities from a colvar file. This action has hidden defaults. More details
 
FILE
the name of the file from which to read these quantities
=COLVARtrim 
VALUES
the values to read from the file
=vol  
IGNORE_TIME
 ignore the time in the colvar file
voltmp: 
READ
Read quantities from a colvar file. This action uses the defaults shown here. More details
 
FILE
the name of the file from which to read these quantities
=COLVARtrim 
VALUES
the values to read from the file
=vol  
IGNORE_TIME
 ignore the time in the colvar file
  
STRIDE
 the frequency with which the file should be read
=1 
EVERY
 only read every nth line of the colvar file
=1

volThe COMBINE action with label vol calculates the following quantities:
 Quantity   
 Type   
 Description  
vol
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=voltmp 
PARAMETERS
 the parameters of the arguments in your function
=10.0 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
renergyThe COMBINE action with label renergy calculates the following quantities:
 Quantity   
 Type   
 Description  
renergy
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=energy 
PARAMETERS
 the parameters of the arguments in your function
=-25000 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
weightsThe REWEIGHT_BIAS action with label weights calculates the following quantities:
 Quantity   
 Type   
 Description  
weights
scalar
the weight to use for this frame to negate the effect the bias: 
REWEIGHT_BIAS
Calculate weights for ensemble averages that negate the effect the bias has on the region of phase space explored More details
 
TEMP
the system temperature
=400 
ARG
 the biases that must be taken into account when reweighting
=b1.bias,uwall.bias

weights350-0The REWEIGHT_TEMP_PRESS action with label weights350-0 calculates the following quantities:
 Quantity   
 Type   
 Description  
weights350-0
scalar
the weight to use for this frame to determine its contribution at a different temperature/pressure: 
REWEIGHT_TEMP_PRESS
Calculate weights for ensemble averages at temperatures and/or pressures different than those used in your original simulation. More details
 
TEMP
the system temperature
=400 
PRESSURE
The system pressure
=301.10704285 
REWEIGHT_TEMP
Reweighting temperature
=350.0 
REWEIGHT_PRESSURE
Reweighting pressure
=0.0 
ENERGY
Energy
=renergy 
VOLUME
Volume
=vol
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights350-0
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh350-0The HISTOGRAM action with label hh350-0 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-0
grid
the estimate of the histogram as a function of the argument that was obtained
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
... HISTOGRAM
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights350-0
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh350-0
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
 
STRIDE
 the frequency with which to store data for averaging
=1
... HISTOGRAM
# PLUMED interprets the command:
# HISTOGRAM ...
#   ARG=refcv.morethan
#   GRID_MIN=-0.5
#   GRID_MAX=250.5
#   GRID_BIN=1000
#   BANDWIDTH=1.
#   LOGWEIGHTS=weights,weights350-0
#   NORMALIZATION=true
#   LABEL=hh350-0
#   CLEAR=10000
# ... HISTOGRAM
# as follows (Click the red comment above to revert to the short version of the input):
hh350-0_wsumThe COMBINE action with label hh350-0_wsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-0_wsum
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=weights,weights350-0 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh350-0_weightThe CUSTOM action with label hh350-0_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-0_weight
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh350-0_wsum 
FUNC
the function you wish to evaluate
=exp(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh350-0_kdeThe KDE action with label hh350-0_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-0_kde
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
ARG
the input for this action is the scalar output from one or more other actions
=refcv.morethan 
GRID_MIN
 the lower bounds for the grid
=-0.5 
GRID_MAX
 the upper bounds for the grid
=250.5 
GRID_BIN
the number of bins for the grid
=1000 
BANDWIDTH
the bandwidths for kernel density esimtation
=1 
hh350-0_kdepThe CUSTOM action with label hh350-0_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-0_kdep
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh350-0_kde,hh350-0_weight 
FUNC
the function you wish to evaluate
=x*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh350-0_uThe ACCUMULATE action with label hh350-0_u calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-0_u
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh350-0_kdep 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh350-0_nsumThe ACCUMULATE action with label hh350-0_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-0_nsum
scalar
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh350-0_weight 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh350-0The CUSTOM action with label hh350-0 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-0
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh350-0_u,hh350-0_nsum 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=hh350-0 
FILE
 the file on which to write the grid
=histo350-0 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f
The DUMPGRID action with label  calculates somethingff350-0The CONVERT_TO_FES action with label ff350-0 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff350-0
grid
the free energy surface: 
CONVERT_TO_FES
Convert a histogram to a free energy surface. This action is a shortcut. More details
 
GRID
the histogram that you would like to convert into a free energy surface (old syntax)
=hh350-0 
TEMP
the temperature at which you are operating
=350.0
# PLUMED interprets the command:
# ff350-0: CONVERT_TO_FES GRID=hh350-0 TEMP=350.0
# as follows (Click the red comment above to revert to the short version of the input):
ff350-0The CUSTOM action with label ff350-0 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff350-0
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh350-0 
FUNC
the function you wish to evaluate
=-2.91006*log(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=ff350-0 
FILE
 the file on which to write the grid
=fes350-0 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f

weights350-1000The REWEIGHT_TEMP_PRESS action with label weights350-1000 calculates the following quantities:
 Quantity   
 Type   
 Description  
weights350-1000
scalar
the weight to use for this frame to determine its contribution at a different temperature/pressure: 
REWEIGHT_TEMP_PRESS
Calculate weights for ensemble averages at temperatures and/or pressures different than those used in your original simulation. More details
 
TEMP
the system temperature
=400 
PRESSURE
The system pressure
=301.10704285 
REWEIGHT_TEMP
Reweighting temperature
=350.0 
REWEIGHT_PRESSURE
Reweighting pressure
=60.22140857 
ENERGY
Energy
=renergy 
VOLUME
Volume
=vol
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights350-1000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh350-1000The HISTOGRAM action with label hh350-1000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-1000
grid
the estimate of the histogram as a function of the argument that was obtained
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
... HISTOGRAM
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights350-1000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh350-1000
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
 
STRIDE
 the frequency with which to store data for averaging
=1
... HISTOGRAM
# PLUMED interprets the command:
# HISTOGRAM ...
#   ARG=refcv.morethan
#   GRID_MIN=-0.5
#   GRID_MAX=250.5
#   GRID_BIN=1000
#   BANDWIDTH=1.
#   LOGWEIGHTS=weights,weights350-1000
#   NORMALIZATION=true
#   LABEL=hh350-1000
#   CLEAR=10000
# ... HISTOGRAM
# as follows (Click the red comment above to revert to the short version of the input):
hh350-1000_wsumThe COMBINE action with label hh350-1000_wsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-1000_wsum
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=weights,weights350-1000 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh350-1000_weightThe CUSTOM action with label hh350-1000_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-1000_weight
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh350-1000_wsum 
FUNC
the function you wish to evaluate
=exp(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh350-1000_kdeThe KDE action with label hh350-1000_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-1000_kde
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
ARG
the input for this action is the scalar output from one or more other actions
=refcv.morethan 
GRID_MIN
 the lower bounds for the grid
=-0.5 
GRID_MAX
 the upper bounds for the grid
=250.5 
GRID_BIN
the number of bins for the grid
=1000 
BANDWIDTH
the bandwidths for kernel density esimtation
=1 
hh350-1000_kdepThe CUSTOM action with label hh350-1000_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-1000_kdep
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh350-1000_kde,hh350-1000_weight 
FUNC
the function you wish to evaluate
=x*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh350-1000_uThe ACCUMULATE action with label hh350-1000_u calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-1000_u
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh350-1000_kdep 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh350-1000_nsumThe ACCUMULATE action with label hh350-1000_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-1000_nsum
scalar
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh350-1000_weight 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh350-1000The CUSTOM action with label hh350-1000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-1000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh350-1000_u,hh350-1000_nsum 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=hh350-1000 
FILE
 the file on which to write the grid
=histo350-1000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f
ff350-1000The CONVERT_TO_FES action with label ff350-1000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff350-1000
grid
the free energy surface: 
CONVERT_TO_FES
Convert a histogram to a free energy surface. This action is a shortcut. More details
 
GRID
the histogram that you would like to convert into a free energy surface (old syntax)
=hh350-1000 
TEMP
the temperature at which you are operating
=350.0
# PLUMED interprets the command:
# ff350-1000: CONVERT_TO_FES GRID=hh350-1000 TEMP=350.0
# as follows (Click the red comment above to revert to the short version of the input):
ff350-1000The CUSTOM action with label ff350-1000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff350-1000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh350-1000 
FUNC
the function you wish to evaluate
=-2.91006*log(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=ff350-1000 
FILE
 the file on which to write the grid
=fes350-1000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f

weights350-2000The REWEIGHT_TEMP_PRESS action with label weights350-2000 calculates the following quantities:
 Quantity   
 Type   
 Description  
weights350-2000
scalar
the weight to use for this frame to determine its contribution at a different temperature/pressure: 
REWEIGHT_TEMP_PRESS
Calculate weights for ensemble averages at temperatures and/or pressures different than those used in your original simulation. More details
 
TEMP
the system temperature
=400 
PRESSURE
The system pressure
=301.10704285 
REWEIGHT_TEMP
Reweighting temperature
=350.0 
REWEIGHT_PRESSURE
Reweighting pressure
=120.44281714 
ENERGY
Energy
=renergy 
VOLUME
Volume
=vol
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights350-2000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh350-2000The HISTOGRAM action with label hh350-2000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-2000
grid
the estimate of the histogram as a function of the argument that was obtained
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
... HISTOGRAM
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights350-2000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh350-2000
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
 
STRIDE
 the frequency with which to store data for averaging
=1
... HISTOGRAM
# PLUMED interprets the command:
# HISTOGRAM ...
#   ARG=refcv.morethan
#   GRID_MIN=-0.5
#   GRID_MAX=250.5
#   GRID_BIN=1000
#   BANDWIDTH=1.
#   LOGWEIGHTS=weights,weights350-2000
#   NORMALIZATION=true
#   LABEL=hh350-2000
#   CLEAR=10000
# ... HISTOGRAM
# as follows (Click the red comment above to revert to the short version of the input):
hh350-2000_wsumThe COMBINE action with label hh350-2000_wsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-2000_wsum
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=weights,weights350-2000 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh350-2000_weightThe CUSTOM action with label hh350-2000_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-2000_weight
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh350-2000_wsum 
FUNC
the function you wish to evaluate
=exp(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh350-2000_kdeThe KDE action with label hh350-2000_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-2000_kde
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
ARG
the input for this action is the scalar output from one or more other actions
=refcv.morethan 
GRID_MIN
 the lower bounds for the grid
=-0.5 
GRID_MAX
 the upper bounds for the grid
=250.5 
GRID_BIN
the number of bins for the grid
=1000 
BANDWIDTH
the bandwidths for kernel density esimtation
=1 
hh350-2000_kdepThe CUSTOM action with label hh350-2000_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-2000_kdep
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh350-2000_kde,hh350-2000_weight 
FUNC
the function you wish to evaluate
=x*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh350-2000_uThe ACCUMULATE action with label hh350-2000_u calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-2000_u
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh350-2000_kdep 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh350-2000_nsumThe ACCUMULATE action with label hh350-2000_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-2000_nsum
scalar
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh350-2000_weight 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh350-2000The CUSTOM action with label hh350-2000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-2000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh350-2000_u,hh350-2000_nsum 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=hh350-2000 
FILE
 the file on which to write the grid
=histo350-2000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f
ff350-2000The CONVERT_TO_FES action with label ff350-2000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff350-2000
grid
the free energy surface: 
CONVERT_TO_FES
Convert a histogram to a free energy surface. This action is a shortcut. More details
 
GRID
the histogram that you would like to convert into a free energy surface (old syntax)
=hh350-2000 
TEMP
the temperature at which you are operating
=350.0
# PLUMED interprets the command:
# ff350-2000: CONVERT_TO_FES GRID=hh350-2000 TEMP=350.0
# as follows (Click the red comment above to revert to the short version of the input):
ff350-2000The CUSTOM action with label ff350-2000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff350-2000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh350-2000 
FUNC
the function you wish to evaluate
=-2.91006*log(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=ff350-2000 
FILE
 the file on which to write the grid
=fes350-2000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f

weights350-3000The REWEIGHT_TEMP_PRESS action with label weights350-3000 calculates the following quantities:
 Quantity   
 Type   
 Description  
weights350-3000
scalar
the weight to use for this frame to determine its contribution at a different temperature/pressure: 
REWEIGHT_TEMP_PRESS
Calculate weights for ensemble averages at temperatures and/or pressures different than those used in your original simulation. More details
 
TEMP
the system temperature
=400 
PRESSURE
The system pressure
=301.10704285 
REWEIGHT_TEMP
Reweighting temperature
=350.0 
REWEIGHT_PRESSURE
Reweighting pressure
=180.66422571 
ENERGY
Energy
=renergy 
VOLUME
Volume
=vol
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights350-3000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh350-3000The HISTOGRAM action with label hh350-3000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-3000
grid
the estimate of the histogram as a function of the argument that was obtained
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
... HISTOGRAM
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights350-3000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh350-3000
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
 
STRIDE
 the frequency with which to store data for averaging
=1
... HISTOGRAM
# PLUMED interprets the command:
# HISTOGRAM ...
#   ARG=refcv.morethan
#   GRID_MIN=-0.5
#   GRID_MAX=250.5
#   GRID_BIN=1000
#   BANDWIDTH=1.
#   LOGWEIGHTS=weights,weights350-3000
#   NORMALIZATION=true
#   LABEL=hh350-3000
#   CLEAR=10000
# ... HISTOGRAM
# as follows (Click the red comment above to revert to the short version of the input):
hh350-3000_wsumThe COMBINE action with label hh350-3000_wsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-3000_wsum
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=weights,weights350-3000 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh350-3000_weightThe CUSTOM action with label hh350-3000_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-3000_weight
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh350-3000_wsum 
FUNC
the function you wish to evaluate
=exp(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh350-3000_kdeThe KDE action with label hh350-3000_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-3000_kde
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
ARG
the input for this action is the scalar output from one or more other actions
=refcv.morethan 
GRID_MIN
 the lower bounds for the grid
=-0.5 
GRID_MAX
 the upper bounds for the grid
=250.5 
GRID_BIN
the number of bins for the grid
=1000 
BANDWIDTH
the bandwidths for kernel density esimtation
=1 
hh350-3000_kdepThe CUSTOM action with label hh350-3000_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-3000_kdep
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh350-3000_kde,hh350-3000_weight 
FUNC
the function you wish to evaluate
=x*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh350-3000_uThe ACCUMULATE action with label hh350-3000_u calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-3000_u
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh350-3000_kdep 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh350-3000_nsumThe ACCUMULATE action with label hh350-3000_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-3000_nsum
scalar
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh350-3000_weight 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh350-3000The CUSTOM action with label hh350-3000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-3000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh350-3000_u,hh350-3000_nsum 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=hh350-3000 
FILE
 the file on which to write the grid
=histo350-3000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f
ff350-3000The CONVERT_TO_FES action with label ff350-3000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff350-3000
grid
the free energy surface: 
CONVERT_TO_FES
Convert a histogram to a free energy surface. This action is a shortcut. More details
 
GRID
the histogram that you would like to convert into a free energy surface (old syntax)
=hh350-3000 
TEMP
the temperature at which you are operating
=350.0
# PLUMED interprets the command:
# ff350-3000: CONVERT_TO_FES GRID=hh350-3000 TEMP=350.0
# as follows (Click the red comment above to revert to the short version of the input):
ff350-3000The CUSTOM action with label ff350-3000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff350-3000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh350-3000 
FUNC
the function you wish to evaluate
=-2.91006*log(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=ff350-3000 
FILE
 the file on which to write the grid
=fes350-3000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f

weights350-4000The REWEIGHT_TEMP_PRESS action with label weights350-4000 calculates the following quantities:
 Quantity   
 Type   
 Description  
weights350-4000
scalar
the weight to use for this frame to determine its contribution at a different temperature/pressure: 
REWEIGHT_TEMP_PRESS
Calculate weights for ensemble averages at temperatures and/or pressures different than those used in your original simulation. More details
 
TEMP
the system temperature
=400 
PRESSURE
The system pressure
=301.10704285 
REWEIGHT_TEMP
Reweighting temperature
=350.0 
REWEIGHT_PRESSURE
Reweighting pressure
=240.88563428 
ENERGY
Energy
=renergy 
VOLUME
Volume
=vol
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights350-4000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh350-4000The HISTOGRAM action with label hh350-4000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-4000
grid
the estimate of the histogram as a function of the argument that was obtained
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
... HISTOGRAM
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights350-4000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh350-4000
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
 
STRIDE
 the frequency with which to store data for averaging
=1
... HISTOGRAM
# PLUMED interprets the command:
# HISTOGRAM ...
#   ARG=refcv.morethan
#   GRID_MIN=-0.5
#   GRID_MAX=250.5
#   GRID_BIN=1000
#   BANDWIDTH=1.
#   LOGWEIGHTS=weights,weights350-4000
#   NORMALIZATION=true
#   LABEL=hh350-4000
#   CLEAR=10000
# ... HISTOGRAM
# as follows (Click the red comment above to revert to the short version of the input):
hh350-4000_wsumThe COMBINE action with label hh350-4000_wsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-4000_wsum
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=weights,weights350-4000 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh350-4000_weightThe CUSTOM action with label hh350-4000_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-4000_weight
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh350-4000_wsum 
FUNC
the function you wish to evaluate
=exp(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh350-4000_kdeThe KDE action with label hh350-4000_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-4000_kde
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
ARG
the input for this action is the scalar output from one or more other actions
=refcv.morethan 
GRID_MIN
 the lower bounds for the grid
=-0.5 
GRID_MAX
 the upper bounds for the grid
=250.5 
GRID_BIN
the number of bins for the grid
=1000 
BANDWIDTH
the bandwidths for kernel density esimtation
=1 
hh350-4000_kdepThe CUSTOM action with label hh350-4000_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-4000_kdep
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh350-4000_kde,hh350-4000_weight 
FUNC
the function you wish to evaluate
=x*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh350-4000_uThe ACCUMULATE action with label hh350-4000_u calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-4000_u
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh350-4000_kdep 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh350-4000_nsumThe ACCUMULATE action with label hh350-4000_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-4000_nsum
scalar
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh350-4000_weight 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh350-4000The CUSTOM action with label hh350-4000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-4000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh350-4000_u,hh350-4000_nsum 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=hh350-4000 
FILE
 the file on which to write the grid
=histo350-4000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f
ff350-4000The CONVERT_TO_FES action with label ff350-4000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff350-4000
grid
the free energy surface: 
CONVERT_TO_FES
Convert a histogram to a free energy surface. This action is a shortcut. More details
 
GRID
the histogram that you would like to convert into a free energy surface (old syntax)
=hh350-4000 
TEMP
the temperature at which you are operating
=350.0
# PLUMED interprets the command:
# ff350-4000: CONVERT_TO_FES GRID=hh350-4000 TEMP=350.0
# as follows (Click the red comment above to revert to the short version of the input):
ff350-4000The CUSTOM action with label ff350-4000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff350-4000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh350-4000 
FUNC
the function you wish to evaluate
=-2.91006*log(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=ff350-4000 
FILE
 the file on which to write the grid
=fes350-4000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f

weights350-5000The REWEIGHT_TEMP_PRESS action with label weights350-5000 calculates the following quantities:
 Quantity   
 Type   
 Description  
weights350-5000
scalar
the weight to use for this frame to determine its contribution at a different temperature/pressure: 
REWEIGHT_TEMP_PRESS
Calculate weights for ensemble averages at temperatures and/or pressures different than those used in your original simulation. More details
 
TEMP
the system temperature
=400 
PRESSURE
The system pressure
=301.10704285 
REWEIGHT_TEMP
Reweighting temperature
=350.0 
REWEIGHT_PRESSURE
Reweighting pressure
=301.10704285 
ENERGY
Energy
=renergy 
VOLUME
Volume
=vol
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights350-5000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh350-5000The HISTOGRAM action with label hh350-5000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-5000
grid
the estimate of the histogram as a function of the argument that was obtained
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
... HISTOGRAM
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights350-5000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh350-5000
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
 
STRIDE
 the frequency with which to store data for averaging
=1
... HISTOGRAM
# PLUMED interprets the command:
# HISTOGRAM ...
#   ARG=refcv.morethan
#   GRID_MIN=-0.5
#   GRID_MAX=250.5
#   GRID_BIN=1000
#   BANDWIDTH=1.
#   LOGWEIGHTS=weights,weights350-5000
#   NORMALIZATION=true
#   LABEL=hh350-5000
#   CLEAR=10000
# ... HISTOGRAM
# as follows (Click the red comment above to revert to the short version of the input):
hh350-5000_wsumThe COMBINE action with label hh350-5000_wsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-5000_wsum
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=weights,weights350-5000 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh350-5000_weightThe CUSTOM action with label hh350-5000_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-5000_weight
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh350-5000_wsum 
FUNC
the function you wish to evaluate
=exp(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh350-5000_kdeThe KDE action with label hh350-5000_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-5000_kde
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
ARG
the input for this action is the scalar output from one or more other actions
=refcv.morethan 
GRID_MIN
 the lower bounds for the grid
=-0.5 
GRID_MAX
 the upper bounds for the grid
=250.5 
GRID_BIN
the number of bins for the grid
=1000 
BANDWIDTH
the bandwidths for kernel density esimtation
=1 
hh350-5000_kdepThe CUSTOM action with label hh350-5000_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-5000_kdep
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh350-5000_kde,hh350-5000_weight 
FUNC
the function you wish to evaluate
=x*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh350-5000_uThe ACCUMULATE action with label hh350-5000_u calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-5000_u
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh350-5000_kdep 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh350-5000_nsumThe ACCUMULATE action with label hh350-5000_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-5000_nsum
scalar
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh350-5000_weight 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh350-5000The CUSTOM action with label hh350-5000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-5000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh350-5000_u,hh350-5000_nsum 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=hh350-5000 
FILE
 the file on which to write the grid
=histo350-5000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f
ff350-5000The CONVERT_TO_FES action with label ff350-5000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff350-5000
grid
the free energy surface: 
CONVERT_TO_FES
Convert a histogram to a free energy surface. This action is a shortcut. More details
 
GRID
the histogram that you would like to convert into a free energy surface (old syntax)
=hh350-5000 
TEMP
the temperature at which you are operating
=350.0
# PLUMED interprets the command:
# ff350-5000: CONVERT_TO_FES GRID=hh350-5000 TEMP=350.0
# as follows (Click the red comment above to revert to the short version of the input):
ff350-5000The CUSTOM action with label ff350-5000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff350-5000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh350-5000 
FUNC
the function you wish to evaluate
=-2.91006*log(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=ff350-5000 
FILE
 the file on which to write the grid
=fes350-5000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f

weights350-6000The REWEIGHT_TEMP_PRESS action with label weights350-6000 calculates the following quantities:
 Quantity   
 Type   
 Description  
weights350-6000
scalar
the weight to use for this frame to determine its contribution at a different temperature/pressure: 
REWEIGHT_TEMP_PRESS
Calculate weights for ensemble averages at temperatures and/or pressures different than those used in your original simulation. More details
 
TEMP
the system temperature
=400 
PRESSURE
The system pressure
=301.10704285 
REWEIGHT_TEMP
Reweighting temperature
=350.0 
REWEIGHT_PRESSURE
Reweighting pressure
=361.32845142 
ENERGY
Energy
=renergy 
VOLUME
Volume
=vol
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights350-6000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh350-6000The HISTOGRAM action with label hh350-6000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-6000
grid
the estimate of the histogram as a function of the argument that was obtained
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
... HISTOGRAM
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights350-6000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh350-6000
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
 
STRIDE
 the frequency with which to store data for averaging
=1
... HISTOGRAM
# PLUMED interprets the command:
# HISTOGRAM ...
#   ARG=refcv.morethan
#   GRID_MIN=-0.5
#   GRID_MAX=250.5
#   GRID_BIN=1000
#   BANDWIDTH=1.
#   LOGWEIGHTS=weights,weights350-6000
#   NORMALIZATION=true
#   LABEL=hh350-6000
#   CLEAR=10000
# ... HISTOGRAM
# as follows (Click the red comment above to revert to the short version of the input):
hh350-6000_wsumThe COMBINE action with label hh350-6000_wsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-6000_wsum
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=weights,weights350-6000 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh350-6000_weightThe CUSTOM action with label hh350-6000_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-6000_weight
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh350-6000_wsum 
FUNC
the function you wish to evaluate
=exp(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh350-6000_kdeThe KDE action with label hh350-6000_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-6000_kde
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
ARG
the input for this action is the scalar output from one or more other actions
=refcv.morethan 
GRID_MIN
 the lower bounds for the grid
=-0.5 
GRID_MAX
 the upper bounds for the grid
=250.5 
GRID_BIN
the number of bins for the grid
=1000 
BANDWIDTH
the bandwidths for kernel density esimtation
=1 
hh350-6000_kdepThe CUSTOM action with label hh350-6000_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-6000_kdep
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh350-6000_kde,hh350-6000_weight 
FUNC
the function you wish to evaluate
=x*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh350-6000_uThe ACCUMULATE action with label hh350-6000_u calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-6000_u
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh350-6000_kdep 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh350-6000_nsumThe ACCUMULATE action with label hh350-6000_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-6000_nsum
scalar
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh350-6000_weight 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh350-6000The CUSTOM action with label hh350-6000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-6000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh350-6000_u,hh350-6000_nsum 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=hh350-6000 
FILE
 the file on which to write the grid
=histo350-6000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f
ff350-6000The CONVERT_TO_FES action with label ff350-6000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff350-6000
grid
the free energy surface: 
CONVERT_TO_FES
Convert a histogram to a free energy surface. This action is a shortcut. More details
 
GRID
the histogram that you would like to convert into a free energy surface (old syntax)
=hh350-6000 
TEMP
the temperature at which you are operating
=350.0
# PLUMED interprets the command:
# ff350-6000: CONVERT_TO_FES GRID=hh350-6000 TEMP=350.0
# as follows (Click the red comment above to revert to the short version of the input):
ff350-6000The CUSTOM action with label ff350-6000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff350-6000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh350-6000 
FUNC
the function you wish to evaluate
=-2.91006*log(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=ff350-6000 
FILE
 the file on which to write the grid
=fes350-6000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f

weights350-7000The REWEIGHT_TEMP_PRESS action with label weights350-7000 calculates the following quantities:
 Quantity   
 Type   
 Description  
weights350-7000
scalar
the weight to use for this frame to determine its contribution at a different temperature/pressure: 
REWEIGHT_TEMP_PRESS
Calculate weights for ensemble averages at temperatures and/or pressures different than those used in your original simulation. More details
 
TEMP
the system temperature
=400 
PRESSURE
The system pressure
=301.10704285 
REWEIGHT_TEMP
Reweighting temperature
=350.0 
REWEIGHT_PRESSURE
Reweighting pressure
=421.54985999 
ENERGY
Energy
=renergy 
VOLUME
Volume
=vol
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights350-7000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh350-7000The HISTOGRAM action with label hh350-7000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-7000
grid
the estimate of the histogram as a function of the argument that was obtained
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
... HISTOGRAM
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights350-7000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh350-7000
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
 
STRIDE
 the frequency with which to store data for averaging
=1
... HISTOGRAM
# PLUMED interprets the command:
# HISTOGRAM ...
#   ARG=refcv.morethan
#   GRID_MIN=-0.5
#   GRID_MAX=250.5
#   GRID_BIN=1000
#   BANDWIDTH=1.
#   LOGWEIGHTS=weights,weights350-7000
#   NORMALIZATION=true
#   LABEL=hh350-7000
#   CLEAR=10000
# ... HISTOGRAM
# as follows (Click the red comment above to revert to the short version of the input):
hh350-7000_wsumThe COMBINE action with label hh350-7000_wsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-7000_wsum
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=weights,weights350-7000 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh350-7000_weightThe CUSTOM action with label hh350-7000_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-7000_weight
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh350-7000_wsum 
FUNC
the function you wish to evaluate
=exp(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh350-7000_kdeThe KDE action with label hh350-7000_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-7000_kde
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
ARG
the input for this action is the scalar output from one or more other actions
=refcv.morethan 
GRID_MIN
 the lower bounds for the grid
=-0.5 
GRID_MAX
 the upper bounds for the grid
=250.5 
GRID_BIN
the number of bins for the grid
=1000 
BANDWIDTH
the bandwidths for kernel density esimtation
=1 
hh350-7000_kdepThe CUSTOM action with label hh350-7000_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-7000_kdep
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh350-7000_kde,hh350-7000_weight 
FUNC
the function you wish to evaluate
=x*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh350-7000_uThe ACCUMULATE action with label hh350-7000_u calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-7000_u
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh350-7000_kdep 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh350-7000_nsumThe ACCUMULATE action with label hh350-7000_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-7000_nsum
scalar
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh350-7000_weight 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh350-7000The CUSTOM action with label hh350-7000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-7000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh350-7000_u,hh350-7000_nsum 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=hh350-7000 
FILE
 the file on which to write the grid
=histo350-7000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f
ff350-7000The CONVERT_TO_FES action with label ff350-7000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff350-7000
grid
the free energy surface: 
CONVERT_TO_FES
Convert a histogram to a free energy surface. This action is a shortcut. More details
 
GRID
the histogram that you would like to convert into a free energy surface (old syntax)
=hh350-7000 
TEMP
the temperature at which you are operating
=350.0
# PLUMED interprets the command:
# ff350-7000: CONVERT_TO_FES GRID=hh350-7000 TEMP=350.0
# as follows (Click the red comment above to revert to the short version of the input):
ff350-7000The CUSTOM action with label ff350-7000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff350-7000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh350-7000 
FUNC
the function you wish to evaluate
=-2.91006*log(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=ff350-7000 
FILE
 the file on which to write the grid
=fes350-7000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f

weights350-8000The REWEIGHT_TEMP_PRESS action with label weights350-8000 calculates the following quantities:
 Quantity   
 Type   
 Description  
weights350-8000
scalar
the weight to use for this frame to determine its contribution at a different temperature/pressure: 
REWEIGHT_TEMP_PRESS
Calculate weights for ensemble averages at temperatures and/or pressures different than those used in your original simulation. More details
 
TEMP
the system temperature
=400 
PRESSURE
The system pressure
=301.10704285 
REWEIGHT_TEMP
Reweighting temperature
=350.0 
REWEIGHT_PRESSURE
Reweighting pressure
=481.77126856 
ENERGY
Energy
=renergy 
VOLUME
Volume
=vol
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights350-8000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh350-8000The HISTOGRAM action with label hh350-8000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-8000
grid
the estimate of the histogram as a function of the argument that was obtained
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
... HISTOGRAM
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights350-8000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh350-8000
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
 
STRIDE
 the frequency with which to store data for averaging
=1
... HISTOGRAM
# PLUMED interprets the command:
# HISTOGRAM ...
#   ARG=refcv.morethan
#   GRID_MIN=-0.5
#   GRID_MAX=250.5
#   GRID_BIN=1000
#   BANDWIDTH=1.
#   LOGWEIGHTS=weights,weights350-8000
#   NORMALIZATION=true
#   LABEL=hh350-8000
#   CLEAR=10000
# ... HISTOGRAM
# as follows (Click the red comment above to revert to the short version of the input):
hh350-8000_wsumThe COMBINE action with label hh350-8000_wsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-8000_wsum
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=weights,weights350-8000 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh350-8000_weightThe CUSTOM action with label hh350-8000_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-8000_weight
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh350-8000_wsum 
FUNC
the function you wish to evaluate
=exp(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh350-8000_kdeThe KDE action with label hh350-8000_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-8000_kde
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
ARG
the input for this action is the scalar output from one or more other actions
=refcv.morethan 
GRID_MIN
 the lower bounds for the grid
=-0.5 
GRID_MAX
 the upper bounds for the grid
=250.5 
GRID_BIN
the number of bins for the grid
=1000 
BANDWIDTH
the bandwidths for kernel density esimtation
=1 
hh350-8000_kdepThe CUSTOM action with label hh350-8000_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-8000_kdep
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh350-8000_kde,hh350-8000_weight 
FUNC
the function you wish to evaluate
=x*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh350-8000_uThe ACCUMULATE action with label hh350-8000_u calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-8000_u
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh350-8000_kdep 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh350-8000_nsumThe ACCUMULATE action with label hh350-8000_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-8000_nsum
scalar
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh350-8000_weight 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh350-8000The CUSTOM action with label hh350-8000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-8000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh350-8000_u,hh350-8000_nsum 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=hh350-8000 
FILE
 the file on which to write the grid
=histo350-8000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f
ff350-8000The CONVERT_TO_FES action with label ff350-8000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff350-8000
grid
the free energy surface: 
CONVERT_TO_FES
Convert a histogram to a free energy surface. This action is a shortcut. More details
 
GRID
the histogram that you would like to convert into a free energy surface (old syntax)
=hh350-8000 
TEMP
the temperature at which you are operating
=350.0
# PLUMED interprets the command:
# ff350-8000: CONVERT_TO_FES GRID=hh350-8000 TEMP=350.0
# as follows (Click the red comment above to revert to the short version of the input):
ff350-8000The CUSTOM action with label ff350-8000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff350-8000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh350-8000 
FUNC
the function you wish to evaluate
=-2.91006*log(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=ff350-8000 
FILE
 the file on which to write the grid
=fes350-8000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f

weights350-9000The REWEIGHT_TEMP_PRESS action with label weights350-9000 calculates the following quantities:
 Quantity   
 Type   
 Description  
weights350-9000
scalar
the weight to use for this frame to determine its contribution at a different temperature/pressure: 
REWEIGHT_TEMP_PRESS
Calculate weights for ensemble averages at temperatures and/or pressures different than those used in your original simulation. More details
 
TEMP
the system temperature
=400 
PRESSURE
The system pressure
=301.10704285 
REWEIGHT_TEMP
Reweighting temperature
=350.0 
REWEIGHT_PRESSURE
Reweighting pressure
=541.9926771300001 
ENERGY
Energy
=renergy 
VOLUME
Volume
=vol
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights350-9000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh350-9000The HISTOGRAM action with label hh350-9000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-9000
grid
the estimate of the histogram as a function of the argument that was obtained
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
... HISTOGRAM
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights350-9000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh350-9000
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
 
STRIDE
 the frequency with which to store data for averaging
=1
... HISTOGRAM
# PLUMED interprets the command:
# HISTOGRAM ...
#   ARG=refcv.morethan
#   GRID_MIN=-0.5
#   GRID_MAX=250.5
#   GRID_BIN=1000
#   BANDWIDTH=1.
#   LOGWEIGHTS=weights,weights350-9000
#   NORMALIZATION=true
#   LABEL=hh350-9000
#   CLEAR=10000
# ... HISTOGRAM
# as follows (Click the red comment above to revert to the short version of the input):
hh350-9000_wsumThe COMBINE action with label hh350-9000_wsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-9000_wsum
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=weights,weights350-9000 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh350-9000_weightThe CUSTOM action with label hh350-9000_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-9000_weight
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh350-9000_wsum 
FUNC
the function you wish to evaluate
=exp(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh350-9000_kdeThe KDE action with label hh350-9000_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-9000_kde
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
ARG
the input for this action is the scalar output from one or more other actions
=refcv.morethan 
GRID_MIN
 the lower bounds for the grid
=-0.5 
GRID_MAX
 the upper bounds for the grid
=250.5 
GRID_BIN
the number of bins for the grid
=1000 
BANDWIDTH
the bandwidths for kernel density esimtation
=1 
hh350-9000_kdepThe CUSTOM action with label hh350-9000_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-9000_kdep
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh350-9000_kde,hh350-9000_weight 
FUNC
the function you wish to evaluate
=x*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh350-9000_uThe ACCUMULATE action with label hh350-9000_u calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-9000_u
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh350-9000_kdep 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh350-9000_nsumThe ACCUMULATE action with label hh350-9000_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-9000_nsum
scalar
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh350-9000_weight 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh350-9000The CUSTOM action with label hh350-9000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-9000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh350-9000_u,hh350-9000_nsum 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=hh350-9000 
FILE
 the file on which to write the grid
=histo350-9000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f
ff350-9000The CONVERT_TO_FES action with label ff350-9000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff350-9000
grid
the free energy surface: 
CONVERT_TO_FES
Convert a histogram to a free energy surface. This action is a shortcut. More details
 
GRID
the histogram that you would like to convert into a free energy surface (old syntax)
=hh350-9000 
TEMP
the temperature at which you are operating
=350.0
# PLUMED interprets the command:
# ff350-9000: CONVERT_TO_FES GRID=hh350-9000 TEMP=350.0
# as follows (Click the red comment above to revert to the short version of the input):
ff350-9000The CUSTOM action with label ff350-9000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff350-9000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh350-9000 
FUNC
the function you wish to evaluate
=-2.91006*log(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=ff350-9000 
FILE
 the file on which to write the grid
=fes350-9000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f

weights350-10000The REWEIGHT_TEMP_PRESS action with label weights350-10000 calculates the following quantities:
 Quantity   
 Type   
 Description  
weights350-10000
scalar
the weight to use for this frame to determine its contribution at a different temperature/pressure: 
REWEIGHT_TEMP_PRESS
Calculate weights for ensemble averages at temperatures and/or pressures different than those used in your original simulation. More details
 
TEMP
the system temperature
=400 
PRESSURE
The system pressure
=301.10704285 
REWEIGHT_TEMP
Reweighting temperature
=350.0 
REWEIGHT_PRESSURE
Reweighting pressure
=602.2140857 
ENERGY
Energy
=renergy 
VOLUME
Volume
=vol
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights350-10000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh350-10000The HISTOGRAM action with label hh350-10000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-10000
grid
the estimate of the histogram as a function of the argument that was obtained
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
... HISTOGRAM
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights350-10000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh350-10000
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
 
STRIDE
 the frequency with which to store data for averaging
=1
... HISTOGRAM
# PLUMED interprets the command:
# HISTOGRAM ...
#   ARG=refcv.morethan
#   GRID_MIN=-0.5
#   GRID_MAX=250.5
#   GRID_BIN=1000
#   BANDWIDTH=1.
#   LOGWEIGHTS=weights,weights350-10000
#   NORMALIZATION=true
#   LABEL=hh350-10000
#   CLEAR=10000
# ... HISTOGRAM
# as follows (Click the red comment above to revert to the short version of the input):
hh350-10000_wsumThe COMBINE action with label hh350-10000_wsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-10000_wsum
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=weights,weights350-10000 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh350-10000_weightThe CUSTOM action with label hh350-10000_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-10000_weight
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh350-10000_wsum 
FUNC
the function you wish to evaluate
=exp(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh350-10000_kdeThe KDE action with label hh350-10000_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-10000_kde
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
ARG
the input for this action is the scalar output from one or more other actions
=refcv.morethan 
GRID_MIN
 the lower bounds for the grid
=-0.5 
GRID_MAX
 the upper bounds for the grid
=250.5 
GRID_BIN
the number of bins for the grid
=1000 
BANDWIDTH
the bandwidths for kernel density esimtation
=1 
hh350-10000_kdepThe CUSTOM action with label hh350-10000_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-10000_kdep
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh350-10000_kde,hh350-10000_weight 
FUNC
the function you wish to evaluate
=x*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh350-10000_uThe ACCUMULATE action with label hh350-10000_u calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-10000_u
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh350-10000_kdep 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh350-10000_nsumThe ACCUMULATE action with label hh350-10000_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-10000_nsum
scalar
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh350-10000_weight 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh350-10000The CUSTOM action with label hh350-10000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh350-10000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh350-10000_u,hh350-10000_nsum 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=hh350-10000 
FILE
 the file on which to write the grid
=histo350-10000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f
ff350-10000The CONVERT_TO_FES action with label ff350-10000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff350-10000
grid
the free energy surface: 
CONVERT_TO_FES
Convert a histogram to a free energy surface. This action is a shortcut. More details
 
GRID
the histogram that you would like to convert into a free energy surface (old syntax)
=hh350-10000 
TEMP
the temperature at which you are operating
=350.0
# PLUMED interprets the command:
# ff350-10000: CONVERT_TO_FES GRID=hh350-10000 TEMP=350.0
# as follows (Click the red comment above to revert to the short version of the input):
ff350-10000The CUSTOM action with label ff350-10000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff350-10000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh350-10000 
FUNC
the function you wish to evaluate
=-2.91006*log(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=ff350-10000 
FILE
 the file on which to write the grid
=fes350-10000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f

weights360-0The REWEIGHT_TEMP_PRESS action with label weights360-0 calculates the following quantities:
 Quantity   
 Type   
 Description  
weights360-0
scalar
the weight to use for this frame to determine its contribution at a different temperature/pressure: 
REWEIGHT_TEMP_PRESS
Calculate weights for ensemble averages at temperatures and/or pressures different than those used in your original simulation. More details
 
TEMP
the system temperature
=400 
PRESSURE
The system pressure
=301.10704285 
REWEIGHT_TEMP
Reweighting temperature
=360.0 
REWEIGHT_PRESSURE
Reweighting pressure
=0.0 
ENERGY
Energy
=renergy 
VOLUME
Volume
=vol
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights360-0
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh360-0The HISTOGRAM action with label hh360-0 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-0
grid
the estimate of the histogram as a function of the argument that was obtained
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
... HISTOGRAM
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights360-0
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh360-0
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
 
STRIDE
 the frequency with which to store data for averaging
=1
... HISTOGRAM
# PLUMED interprets the command:
# HISTOGRAM ...
#   ARG=refcv.morethan
#   GRID_MIN=-0.5
#   GRID_MAX=250.5
#   GRID_BIN=1000
#   BANDWIDTH=1.
#   LOGWEIGHTS=weights,weights360-0
#   NORMALIZATION=true
#   LABEL=hh360-0
#   CLEAR=10000
# ... HISTOGRAM
# as follows (Click the red comment above to revert to the short version of the input):
hh360-0_wsumThe COMBINE action with label hh360-0_wsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-0_wsum
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=weights,weights360-0 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh360-0_weightThe CUSTOM action with label hh360-0_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-0_weight
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh360-0_wsum 
FUNC
the function you wish to evaluate
=exp(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh360-0_kdeThe KDE action with label hh360-0_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-0_kde
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
ARG
the input for this action is the scalar output from one or more other actions
=refcv.morethan 
GRID_MIN
 the lower bounds for the grid
=-0.5 
GRID_MAX
 the upper bounds for the grid
=250.5 
GRID_BIN
the number of bins for the grid
=1000 
BANDWIDTH
the bandwidths for kernel density esimtation
=1 
hh360-0_kdepThe CUSTOM action with label hh360-0_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-0_kdep
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh360-0_kde,hh360-0_weight 
FUNC
the function you wish to evaluate
=x*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh360-0_uThe ACCUMULATE action with label hh360-0_u calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-0_u
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh360-0_kdep 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh360-0_nsumThe ACCUMULATE action with label hh360-0_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-0_nsum
scalar
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh360-0_weight 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh360-0The CUSTOM action with label hh360-0 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-0
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh360-0_u,hh360-0_nsum 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=hh360-0 
FILE
 the file on which to write the grid
=histo360-0 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f
ff360-0The CONVERT_TO_FES action with label ff360-0 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff360-0
grid
the free energy surface: 
CONVERT_TO_FES
Convert a histogram to a free energy surface. This action is a shortcut. More details
 
GRID
the histogram that you would like to convert into a free energy surface (old syntax)
=hh360-0 
TEMP
the temperature at which you are operating
=360.0
# PLUMED interprets the command:
# ff360-0: CONVERT_TO_FES GRID=hh360-0 TEMP=360.0
# as follows (Click the red comment above to revert to the short version of the input):
ff360-0The CUSTOM action with label ff360-0 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff360-0
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh360-0 
FUNC
the function you wish to evaluate
=-2.99321*log(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=ff360-0 
FILE
 the file on which to write the grid
=fes360-0 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f

weights360-1000The REWEIGHT_TEMP_PRESS action with label weights360-1000 calculates the following quantities:
 Quantity   
 Type   
 Description  
weights360-1000
scalar
the weight to use for this frame to determine its contribution at a different temperature/pressure: 
REWEIGHT_TEMP_PRESS
Calculate weights for ensemble averages at temperatures and/or pressures different than those used in your original simulation. More details
 
TEMP
the system temperature
=400 
PRESSURE
The system pressure
=301.10704285 
REWEIGHT_TEMP
Reweighting temperature
=360.0 
REWEIGHT_PRESSURE
Reweighting pressure
=60.22140857 
ENERGY
Energy
=renergy 
VOLUME
Volume
=vol
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights360-1000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh360-1000The HISTOGRAM action with label hh360-1000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-1000
grid
the estimate of the histogram as a function of the argument that was obtained
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
... HISTOGRAM
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights360-1000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh360-1000
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
 
STRIDE
 the frequency with which to store data for averaging
=1
... HISTOGRAM
# PLUMED interprets the command:
# HISTOGRAM ...
#   ARG=refcv.morethan
#   GRID_MIN=-0.5
#   GRID_MAX=250.5
#   GRID_BIN=1000
#   BANDWIDTH=1.
#   LOGWEIGHTS=weights,weights360-1000
#   NORMALIZATION=true
#   LABEL=hh360-1000
#   CLEAR=10000
# ... HISTOGRAM
# as follows (Click the red comment above to revert to the short version of the input):
hh360-1000_wsumThe COMBINE action with label hh360-1000_wsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-1000_wsum
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=weights,weights360-1000 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh360-1000_weightThe CUSTOM action with label hh360-1000_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-1000_weight
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh360-1000_wsum 
FUNC
the function you wish to evaluate
=exp(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh360-1000_kdeThe KDE action with label hh360-1000_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-1000_kde
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
ARG
the input for this action is the scalar output from one or more other actions
=refcv.morethan 
GRID_MIN
 the lower bounds for the grid
=-0.5 
GRID_MAX
 the upper bounds for the grid
=250.5 
GRID_BIN
the number of bins for the grid
=1000 
BANDWIDTH
the bandwidths for kernel density esimtation
=1 
hh360-1000_kdepThe CUSTOM action with label hh360-1000_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-1000_kdep
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh360-1000_kde,hh360-1000_weight 
FUNC
the function you wish to evaluate
=x*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh360-1000_uThe ACCUMULATE action with label hh360-1000_u calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-1000_u
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh360-1000_kdep 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh360-1000_nsumThe ACCUMULATE action with label hh360-1000_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-1000_nsum
scalar
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh360-1000_weight 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh360-1000The CUSTOM action with label hh360-1000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-1000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh360-1000_u,hh360-1000_nsum 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=hh360-1000 
FILE
 the file on which to write the grid
=histo360-1000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f
ff360-1000The CONVERT_TO_FES action with label ff360-1000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff360-1000
grid
the free energy surface: 
CONVERT_TO_FES
Convert a histogram to a free energy surface. This action is a shortcut. More details
 
GRID
the histogram that you would like to convert into a free energy surface (old syntax)
=hh360-1000 
TEMP
the temperature at which you are operating
=360.0
# PLUMED interprets the command:
# ff360-1000: CONVERT_TO_FES GRID=hh360-1000 TEMP=360.0
# as follows (Click the red comment above to revert to the short version of the input):
ff360-1000The CUSTOM action with label ff360-1000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff360-1000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh360-1000 
FUNC
the function you wish to evaluate
=-2.99321*log(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=ff360-1000 
FILE
 the file on which to write the grid
=fes360-1000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f

weights360-2000The REWEIGHT_TEMP_PRESS action with label weights360-2000 calculates the following quantities:
 Quantity   
 Type   
 Description  
weights360-2000
scalar
the weight to use for this frame to determine its contribution at a different temperature/pressure: 
REWEIGHT_TEMP_PRESS
Calculate weights for ensemble averages at temperatures and/or pressures different than those used in your original simulation. More details
 
TEMP
the system temperature
=400 
PRESSURE
The system pressure
=301.10704285 
REWEIGHT_TEMP
Reweighting temperature
=360.0 
REWEIGHT_PRESSURE
Reweighting pressure
=120.44281714 
ENERGY
Energy
=renergy 
VOLUME
Volume
=vol
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights360-2000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh360-2000The HISTOGRAM action with label hh360-2000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-2000
grid
the estimate of the histogram as a function of the argument that was obtained
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
... HISTOGRAM
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights360-2000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh360-2000
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
 
STRIDE
 the frequency with which to store data for averaging
=1
... HISTOGRAM
# PLUMED interprets the command:
# HISTOGRAM ...
#   ARG=refcv.morethan
#   GRID_MIN=-0.5
#   GRID_MAX=250.5
#   GRID_BIN=1000
#   BANDWIDTH=1.
#   LOGWEIGHTS=weights,weights360-2000
#   NORMALIZATION=true
#   LABEL=hh360-2000
#   CLEAR=10000
# ... HISTOGRAM
# as follows (Click the red comment above to revert to the short version of the input):
hh360-2000_wsumThe COMBINE action with label hh360-2000_wsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-2000_wsum
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=weights,weights360-2000 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh360-2000_weightThe CUSTOM action with label hh360-2000_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-2000_weight
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh360-2000_wsum 
FUNC
the function you wish to evaluate
=exp(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh360-2000_kdeThe KDE action with label hh360-2000_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-2000_kde
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
ARG
the input for this action is the scalar output from one or more other actions
=refcv.morethan 
GRID_MIN
 the lower bounds for the grid
=-0.5 
GRID_MAX
 the upper bounds for the grid
=250.5 
GRID_BIN
the number of bins for the grid
=1000 
BANDWIDTH
the bandwidths for kernel density esimtation
=1 
hh360-2000_kdepThe CUSTOM action with label hh360-2000_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-2000_kdep
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh360-2000_kde,hh360-2000_weight 
FUNC
the function you wish to evaluate
=x*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh360-2000_uThe ACCUMULATE action with label hh360-2000_u calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-2000_u
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh360-2000_kdep 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh360-2000_nsumThe ACCUMULATE action with label hh360-2000_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-2000_nsum
scalar
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh360-2000_weight 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh360-2000The CUSTOM action with label hh360-2000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-2000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh360-2000_u,hh360-2000_nsum 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=hh360-2000 
FILE
 the file on which to write the grid
=histo360-2000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f
ff360-2000The CONVERT_TO_FES action with label ff360-2000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff360-2000
grid
the free energy surface: 
CONVERT_TO_FES
Convert a histogram to a free energy surface. This action is a shortcut. More details
 
GRID
the histogram that you would like to convert into a free energy surface (old syntax)
=hh360-2000 
TEMP
the temperature at which you are operating
=360.0
# PLUMED interprets the command:
# ff360-2000: CONVERT_TO_FES GRID=hh360-2000 TEMP=360.0
# as follows (Click the red comment above to revert to the short version of the input):
ff360-2000The CUSTOM action with label ff360-2000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff360-2000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh360-2000 
FUNC
the function you wish to evaluate
=-2.99321*log(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=ff360-2000 
FILE
 the file on which to write the grid
=fes360-2000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f

weights360-3000The REWEIGHT_TEMP_PRESS action with label weights360-3000 calculates the following quantities:
 Quantity   
 Type   
 Description  
weights360-3000
scalar
the weight to use for this frame to determine its contribution at a different temperature/pressure: 
REWEIGHT_TEMP_PRESS
Calculate weights for ensemble averages at temperatures and/or pressures different than those used in your original simulation. More details
 
TEMP
the system temperature
=400 
PRESSURE
The system pressure
=301.10704285 
REWEIGHT_TEMP
Reweighting temperature
=360.0 
REWEIGHT_PRESSURE
Reweighting pressure
=180.66422571 
ENERGY
Energy
=renergy 
VOLUME
Volume
=vol
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights360-3000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh360-3000The HISTOGRAM action with label hh360-3000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-3000
grid
the estimate of the histogram as a function of the argument that was obtained
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
... HISTOGRAM
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights360-3000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh360-3000
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
 
STRIDE
 the frequency with which to store data for averaging
=1
... HISTOGRAM
# PLUMED interprets the command:
# HISTOGRAM ...
#   ARG=refcv.morethan
#   GRID_MIN=-0.5
#   GRID_MAX=250.5
#   GRID_BIN=1000
#   BANDWIDTH=1.
#   LOGWEIGHTS=weights,weights360-3000
#   NORMALIZATION=true
#   LABEL=hh360-3000
#   CLEAR=10000
# ... HISTOGRAM
# as follows (Click the red comment above to revert to the short version of the input):
hh360-3000_wsumThe COMBINE action with label hh360-3000_wsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-3000_wsum
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=weights,weights360-3000 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh360-3000_weightThe CUSTOM action with label hh360-3000_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-3000_weight
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh360-3000_wsum 
FUNC
the function you wish to evaluate
=exp(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh360-3000_kdeThe KDE action with label hh360-3000_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-3000_kde
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
ARG
the input for this action is the scalar output from one or more other actions
=refcv.morethan 
GRID_MIN
 the lower bounds for the grid
=-0.5 
GRID_MAX
 the upper bounds for the grid
=250.5 
GRID_BIN
the number of bins for the grid
=1000 
BANDWIDTH
the bandwidths for kernel density esimtation
=1 
hh360-3000_kdepThe CUSTOM action with label hh360-3000_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-3000_kdep
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh360-3000_kde,hh360-3000_weight 
FUNC
the function you wish to evaluate
=x*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh360-3000_uThe ACCUMULATE action with label hh360-3000_u calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-3000_u
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh360-3000_kdep 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh360-3000_nsumThe ACCUMULATE action with label hh360-3000_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-3000_nsum
scalar
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh360-3000_weight 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh360-3000The CUSTOM action with label hh360-3000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-3000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh360-3000_u,hh360-3000_nsum 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=hh360-3000 
FILE
 the file on which to write the grid
=histo360-3000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f
ff360-3000The CONVERT_TO_FES action with label ff360-3000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff360-3000
grid
the free energy surface: 
CONVERT_TO_FES
Convert a histogram to a free energy surface. This action is a shortcut. More details
 
GRID
the histogram that you would like to convert into a free energy surface (old syntax)
=hh360-3000 
TEMP
the temperature at which you are operating
=360.0
# PLUMED interprets the command:
# ff360-3000: CONVERT_TO_FES GRID=hh360-3000 TEMP=360.0
# as follows (Click the red comment above to revert to the short version of the input):
ff360-3000The CUSTOM action with label ff360-3000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff360-3000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh360-3000 
FUNC
the function you wish to evaluate
=-2.99321*log(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=ff360-3000 
FILE
 the file on which to write the grid
=fes360-3000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f

weights360-4000The REWEIGHT_TEMP_PRESS action with label weights360-4000 calculates the following quantities:
 Quantity   
 Type   
 Description  
weights360-4000
scalar
the weight to use for this frame to determine its contribution at a different temperature/pressure: 
REWEIGHT_TEMP_PRESS
Calculate weights for ensemble averages at temperatures and/or pressures different than those used in your original simulation. More details
 
TEMP
the system temperature
=400 
PRESSURE
The system pressure
=301.10704285 
REWEIGHT_TEMP
Reweighting temperature
=360.0 
REWEIGHT_PRESSURE
Reweighting pressure
=240.88563428 
ENERGY
Energy
=renergy 
VOLUME
Volume
=vol
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights360-4000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh360-4000The HISTOGRAM action with label hh360-4000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-4000
grid
the estimate of the histogram as a function of the argument that was obtained
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
... HISTOGRAM
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights360-4000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh360-4000
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
 
STRIDE
 the frequency with which to store data for averaging
=1
... HISTOGRAM
# PLUMED interprets the command:
# HISTOGRAM ...
#   ARG=refcv.morethan
#   GRID_MIN=-0.5
#   GRID_MAX=250.5
#   GRID_BIN=1000
#   BANDWIDTH=1.
#   LOGWEIGHTS=weights,weights360-4000
#   NORMALIZATION=true
#   LABEL=hh360-4000
#   CLEAR=10000
# ... HISTOGRAM
# as follows (Click the red comment above to revert to the short version of the input):
hh360-4000_wsumThe COMBINE action with label hh360-4000_wsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-4000_wsum
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=weights,weights360-4000 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh360-4000_weightThe CUSTOM action with label hh360-4000_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-4000_weight
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh360-4000_wsum 
FUNC
the function you wish to evaluate
=exp(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh360-4000_kdeThe KDE action with label hh360-4000_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-4000_kde
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
ARG
the input for this action is the scalar output from one or more other actions
=refcv.morethan 
GRID_MIN
 the lower bounds for the grid
=-0.5 
GRID_MAX
 the upper bounds for the grid
=250.5 
GRID_BIN
the number of bins for the grid
=1000 
BANDWIDTH
the bandwidths for kernel density esimtation
=1 
hh360-4000_kdepThe CUSTOM action with label hh360-4000_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-4000_kdep
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh360-4000_kde,hh360-4000_weight 
FUNC
the function you wish to evaluate
=x*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh360-4000_uThe ACCUMULATE action with label hh360-4000_u calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-4000_u
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh360-4000_kdep 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh360-4000_nsumThe ACCUMULATE action with label hh360-4000_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-4000_nsum
scalar
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh360-4000_weight 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh360-4000The CUSTOM action with label hh360-4000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-4000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh360-4000_u,hh360-4000_nsum 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=hh360-4000 
FILE
 the file on which to write the grid
=histo360-4000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f
ff360-4000The CONVERT_TO_FES action with label ff360-4000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff360-4000
grid
the free energy surface: 
CONVERT_TO_FES
Convert a histogram to a free energy surface. This action is a shortcut. More details
 
GRID
the histogram that you would like to convert into a free energy surface (old syntax)
=hh360-4000 
TEMP
the temperature at which you are operating
=360.0
# PLUMED interprets the command:
# ff360-4000: CONVERT_TO_FES GRID=hh360-4000 TEMP=360.0
# as follows (Click the red comment above to revert to the short version of the input):
ff360-4000The CUSTOM action with label ff360-4000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff360-4000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh360-4000 
FUNC
the function you wish to evaluate
=-2.99321*log(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=ff360-4000 
FILE
 the file on which to write the grid
=fes360-4000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f

weights360-5000The REWEIGHT_TEMP_PRESS action with label weights360-5000 calculates the following quantities:
 Quantity   
 Type   
 Description  
weights360-5000
scalar
the weight to use for this frame to determine its contribution at a different temperature/pressure: 
REWEIGHT_TEMP_PRESS
Calculate weights for ensemble averages at temperatures and/or pressures different than those used in your original simulation. More details
 
TEMP
the system temperature
=400 
PRESSURE
The system pressure
=301.10704285 
REWEIGHT_TEMP
Reweighting temperature
=360.0 
REWEIGHT_PRESSURE
Reweighting pressure
=301.10704285 
ENERGY
Energy
=renergy 
VOLUME
Volume
=vol
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights360-5000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh360-5000The HISTOGRAM action with label hh360-5000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-5000
grid
the estimate of the histogram as a function of the argument that was obtained
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
... HISTOGRAM
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights360-5000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh360-5000
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
 
STRIDE
 the frequency with which to store data for averaging
=1
... HISTOGRAM
# PLUMED interprets the command:
# HISTOGRAM ...
#   ARG=refcv.morethan
#   GRID_MIN=-0.5
#   GRID_MAX=250.5
#   GRID_BIN=1000
#   BANDWIDTH=1.
#   LOGWEIGHTS=weights,weights360-5000
#   NORMALIZATION=true
#   LABEL=hh360-5000
#   CLEAR=10000
# ... HISTOGRAM
# as follows (Click the red comment above to revert to the short version of the input):
hh360-5000_wsumThe COMBINE action with label hh360-5000_wsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-5000_wsum
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=weights,weights360-5000 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh360-5000_weightThe CUSTOM action with label hh360-5000_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-5000_weight
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh360-5000_wsum 
FUNC
the function you wish to evaluate
=exp(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh360-5000_kdeThe KDE action with label hh360-5000_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-5000_kde
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
ARG
the input for this action is the scalar output from one or more other actions
=refcv.morethan 
GRID_MIN
 the lower bounds for the grid
=-0.5 
GRID_MAX
 the upper bounds for the grid
=250.5 
GRID_BIN
the number of bins for the grid
=1000 
BANDWIDTH
the bandwidths for kernel density esimtation
=1 
hh360-5000_kdepThe CUSTOM action with label hh360-5000_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-5000_kdep
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh360-5000_kde,hh360-5000_weight 
FUNC
the function you wish to evaluate
=x*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh360-5000_uThe ACCUMULATE action with label hh360-5000_u calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-5000_u
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh360-5000_kdep 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh360-5000_nsumThe ACCUMULATE action with label hh360-5000_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-5000_nsum
scalar
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh360-5000_weight 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh360-5000The CUSTOM action with label hh360-5000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-5000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh360-5000_u,hh360-5000_nsum 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=hh360-5000 
FILE
 the file on which to write the grid
=histo360-5000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f
ff360-5000The CONVERT_TO_FES action with label ff360-5000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff360-5000
grid
the free energy surface: 
CONVERT_TO_FES
Convert a histogram to a free energy surface. This action is a shortcut. More details
 
GRID
the histogram that you would like to convert into a free energy surface (old syntax)
=hh360-5000 
TEMP
the temperature at which you are operating
=360.0
# PLUMED interprets the command:
# ff360-5000: CONVERT_TO_FES GRID=hh360-5000 TEMP=360.0
# as follows (Click the red comment above to revert to the short version of the input):
ff360-5000The CUSTOM action with label ff360-5000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff360-5000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh360-5000 
FUNC
the function you wish to evaluate
=-2.99321*log(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=ff360-5000 
FILE
 the file on which to write the grid
=fes360-5000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f

weights360-6000The REWEIGHT_TEMP_PRESS action with label weights360-6000 calculates the following quantities:
 Quantity   
 Type   
 Description  
weights360-6000
scalar
the weight to use for this frame to determine its contribution at a different temperature/pressure: 
REWEIGHT_TEMP_PRESS
Calculate weights for ensemble averages at temperatures and/or pressures different than those used in your original simulation. More details
 
TEMP
the system temperature
=400 
PRESSURE
The system pressure
=301.10704285 
REWEIGHT_TEMP
Reweighting temperature
=360.0 
REWEIGHT_PRESSURE
Reweighting pressure
=361.32845142 
ENERGY
Energy
=renergy 
VOLUME
Volume
=vol
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights360-6000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh360-6000The HISTOGRAM action with label hh360-6000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-6000
grid
the estimate of the histogram as a function of the argument that was obtained
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
... HISTOGRAM
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights360-6000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh360-6000
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
 
STRIDE
 the frequency with which to store data for averaging
=1
... HISTOGRAM
# PLUMED interprets the command:
# HISTOGRAM ...
#   ARG=refcv.morethan
#   GRID_MIN=-0.5
#   GRID_MAX=250.5
#   GRID_BIN=1000
#   BANDWIDTH=1.
#   LOGWEIGHTS=weights,weights360-6000
#   NORMALIZATION=true
#   LABEL=hh360-6000
#   CLEAR=10000
# ... HISTOGRAM
# as follows (Click the red comment above to revert to the short version of the input):
hh360-6000_wsumThe COMBINE action with label hh360-6000_wsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-6000_wsum
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=weights,weights360-6000 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh360-6000_weightThe CUSTOM action with label hh360-6000_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-6000_weight
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh360-6000_wsum 
FUNC
the function you wish to evaluate
=exp(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh360-6000_kdeThe KDE action with label hh360-6000_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-6000_kde
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
ARG
the input for this action is the scalar output from one or more other actions
=refcv.morethan 
GRID_MIN
 the lower bounds for the grid
=-0.5 
GRID_MAX
 the upper bounds for the grid
=250.5 
GRID_BIN
the number of bins for the grid
=1000 
BANDWIDTH
the bandwidths for kernel density esimtation
=1 
hh360-6000_kdepThe CUSTOM action with label hh360-6000_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-6000_kdep
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh360-6000_kde,hh360-6000_weight 
FUNC
the function you wish to evaluate
=x*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh360-6000_uThe ACCUMULATE action with label hh360-6000_u calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-6000_u
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh360-6000_kdep 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh360-6000_nsumThe ACCUMULATE action with label hh360-6000_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-6000_nsum
scalar
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh360-6000_weight 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh360-6000The CUSTOM action with label hh360-6000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-6000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh360-6000_u,hh360-6000_nsum 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=hh360-6000 
FILE
 the file on which to write the grid
=histo360-6000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f
ff360-6000The CONVERT_TO_FES action with label ff360-6000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff360-6000
grid
the free energy surface: 
CONVERT_TO_FES
Convert a histogram to a free energy surface. This action is a shortcut. More details
 
GRID
the histogram that you would like to convert into a free energy surface (old syntax)
=hh360-6000 
TEMP
the temperature at which you are operating
=360.0
# PLUMED interprets the command:
# ff360-6000: CONVERT_TO_FES GRID=hh360-6000 TEMP=360.0
# as follows (Click the red comment above to revert to the short version of the input):
ff360-6000The CUSTOM action with label ff360-6000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff360-6000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh360-6000 
FUNC
the function you wish to evaluate
=-2.99321*log(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=ff360-6000 
FILE
 the file on which to write the grid
=fes360-6000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f

weights360-7000The REWEIGHT_TEMP_PRESS action with label weights360-7000 calculates the following quantities:
 Quantity   
 Type   
 Description  
weights360-7000
scalar
the weight to use for this frame to determine its contribution at a different temperature/pressure: 
REWEIGHT_TEMP_PRESS
Calculate weights for ensemble averages at temperatures and/or pressures different than those used in your original simulation. More details
 
TEMP
the system temperature
=400 
PRESSURE
The system pressure
=301.10704285 
REWEIGHT_TEMP
Reweighting temperature
=360.0 
REWEIGHT_PRESSURE
Reweighting pressure
=421.54985999 
ENERGY
Energy
=renergy 
VOLUME
Volume
=vol
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights360-7000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh360-7000The HISTOGRAM action with label hh360-7000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-7000
grid
the estimate of the histogram as a function of the argument that was obtained
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
... HISTOGRAM
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights360-7000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh360-7000
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
 
STRIDE
 the frequency with which to store data for averaging
=1
... HISTOGRAM
# PLUMED interprets the command:
# HISTOGRAM ...
#   ARG=refcv.morethan
#   GRID_MIN=-0.5
#   GRID_MAX=250.5
#   GRID_BIN=1000
#   BANDWIDTH=1.
#   LOGWEIGHTS=weights,weights360-7000
#   NORMALIZATION=true
#   LABEL=hh360-7000
#   CLEAR=10000
# ... HISTOGRAM
# as follows (Click the red comment above to revert to the short version of the input):
hh360-7000_wsumThe COMBINE action with label hh360-7000_wsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-7000_wsum
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=weights,weights360-7000 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh360-7000_weightThe CUSTOM action with label hh360-7000_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-7000_weight
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh360-7000_wsum 
FUNC
the function you wish to evaluate
=exp(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh360-7000_kdeThe KDE action with label hh360-7000_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-7000_kde
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
ARG
the input for this action is the scalar output from one or more other actions
=refcv.morethan 
GRID_MIN
 the lower bounds for the grid
=-0.5 
GRID_MAX
 the upper bounds for the grid
=250.5 
GRID_BIN
the number of bins for the grid
=1000 
BANDWIDTH
the bandwidths for kernel density esimtation
=1 
hh360-7000_kdepThe CUSTOM action with label hh360-7000_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-7000_kdep
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh360-7000_kde,hh360-7000_weight 
FUNC
the function you wish to evaluate
=x*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh360-7000_uThe ACCUMULATE action with label hh360-7000_u calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-7000_u
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh360-7000_kdep 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh360-7000_nsumThe ACCUMULATE action with label hh360-7000_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-7000_nsum
scalar
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh360-7000_weight 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh360-7000The CUSTOM action with label hh360-7000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-7000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh360-7000_u,hh360-7000_nsum 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=hh360-7000 
FILE
 the file on which to write the grid
=histo360-7000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f
ff360-7000The CONVERT_TO_FES action with label ff360-7000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff360-7000
grid
the free energy surface: 
CONVERT_TO_FES
Convert a histogram to a free energy surface. This action is a shortcut. More details
 
GRID
the histogram that you would like to convert into a free energy surface (old syntax)
=hh360-7000 
TEMP
the temperature at which you are operating
=360.0
# PLUMED interprets the command:
# ff360-7000: CONVERT_TO_FES GRID=hh360-7000 TEMP=360.0
# as follows (Click the red comment above to revert to the short version of the input):
ff360-7000The CUSTOM action with label ff360-7000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff360-7000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh360-7000 
FUNC
the function you wish to evaluate
=-2.99321*log(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=ff360-7000 
FILE
 the file on which to write the grid
=fes360-7000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f

weights360-8000The REWEIGHT_TEMP_PRESS action with label weights360-8000 calculates the following quantities:
 Quantity   
 Type   
 Description  
weights360-8000
scalar
the weight to use for this frame to determine its contribution at a different temperature/pressure: 
REWEIGHT_TEMP_PRESS
Calculate weights for ensemble averages at temperatures and/or pressures different than those used in your original simulation. More details
 
TEMP
the system temperature
=400 
PRESSURE
The system pressure
=301.10704285 
REWEIGHT_TEMP
Reweighting temperature
=360.0 
REWEIGHT_PRESSURE
Reweighting pressure
=481.77126856 
ENERGY
Energy
=renergy 
VOLUME
Volume
=vol
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights360-8000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh360-8000The HISTOGRAM action with label hh360-8000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-8000
grid
the estimate of the histogram as a function of the argument that was obtained
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
... HISTOGRAM
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights360-8000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh360-8000
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
 
STRIDE
 the frequency with which to store data for averaging
=1
... HISTOGRAM
# PLUMED interprets the command:
# HISTOGRAM ...
#   ARG=refcv.morethan
#   GRID_MIN=-0.5
#   GRID_MAX=250.5
#   GRID_BIN=1000
#   BANDWIDTH=1.
#   LOGWEIGHTS=weights,weights360-8000
#   NORMALIZATION=true
#   LABEL=hh360-8000
#   CLEAR=10000
# ... HISTOGRAM
# as follows (Click the red comment above to revert to the short version of the input):
hh360-8000_wsumThe COMBINE action with label hh360-8000_wsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-8000_wsum
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=weights,weights360-8000 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh360-8000_weightThe CUSTOM action with label hh360-8000_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-8000_weight
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh360-8000_wsum 
FUNC
the function you wish to evaluate
=exp(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh360-8000_kdeThe KDE action with label hh360-8000_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-8000_kde
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
ARG
the input for this action is the scalar output from one or more other actions
=refcv.morethan 
GRID_MIN
 the lower bounds for the grid
=-0.5 
GRID_MAX
 the upper bounds for the grid
=250.5 
GRID_BIN
the number of bins for the grid
=1000 
BANDWIDTH
the bandwidths for kernel density esimtation
=1 
hh360-8000_kdepThe CUSTOM action with label hh360-8000_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-8000_kdep
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh360-8000_kde,hh360-8000_weight 
FUNC
the function you wish to evaluate
=x*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh360-8000_uThe ACCUMULATE action with label hh360-8000_u calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-8000_u
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh360-8000_kdep 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh360-8000_nsumThe ACCUMULATE action with label hh360-8000_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-8000_nsum
scalar
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh360-8000_weight 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh360-8000The CUSTOM action with label hh360-8000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-8000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh360-8000_u,hh360-8000_nsum 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=hh360-8000 
FILE
 the file on which to write the grid
=histo360-8000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f
ff360-8000The CONVERT_TO_FES action with label ff360-8000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff360-8000
grid
the free energy surface: 
CONVERT_TO_FES
Convert a histogram to a free energy surface. This action is a shortcut. More details
 
GRID
the histogram that you would like to convert into a free energy surface (old syntax)
=hh360-8000 
TEMP
the temperature at which you are operating
=360.0
# PLUMED interprets the command:
# ff360-8000: CONVERT_TO_FES GRID=hh360-8000 TEMP=360.0
# as follows (Click the red comment above to revert to the short version of the input):
ff360-8000The CUSTOM action with label ff360-8000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff360-8000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh360-8000 
FUNC
the function you wish to evaluate
=-2.99321*log(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=ff360-8000 
FILE
 the file on which to write the grid
=fes360-8000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f

weights360-9000The REWEIGHT_TEMP_PRESS action with label weights360-9000 calculates the following quantities:
 Quantity   
 Type   
 Description  
weights360-9000
scalar
the weight to use for this frame to determine its contribution at a different temperature/pressure: 
REWEIGHT_TEMP_PRESS
Calculate weights for ensemble averages at temperatures and/or pressures different than those used in your original simulation. More details
 
TEMP
the system temperature
=400 
PRESSURE
The system pressure
=301.10704285 
REWEIGHT_TEMP
Reweighting temperature
=360.0 
REWEIGHT_PRESSURE
Reweighting pressure
=541.9926771300001 
ENERGY
Energy
=renergy 
VOLUME
Volume
=vol
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights360-9000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh360-9000The HISTOGRAM action with label hh360-9000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-9000
grid
the estimate of the histogram as a function of the argument that was obtained
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
... HISTOGRAM
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights360-9000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh360-9000
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
 
STRIDE
 the frequency with which to store data for averaging
=1
... HISTOGRAM
# PLUMED interprets the command:
# HISTOGRAM ...
#   ARG=refcv.morethan
#   GRID_MIN=-0.5
#   GRID_MAX=250.5
#   GRID_BIN=1000
#   BANDWIDTH=1.
#   LOGWEIGHTS=weights,weights360-9000
#   NORMALIZATION=true
#   LABEL=hh360-9000
#   CLEAR=10000
# ... HISTOGRAM
# as follows (Click the red comment above to revert to the short version of the input):
hh360-9000_wsumThe COMBINE action with label hh360-9000_wsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-9000_wsum
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=weights,weights360-9000 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh360-9000_weightThe CUSTOM action with label hh360-9000_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-9000_weight
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh360-9000_wsum 
FUNC
the function you wish to evaluate
=exp(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh360-9000_kdeThe KDE action with label hh360-9000_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-9000_kde
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
ARG
the input for this action is the scalar output from one or more other actions
=refcv.morethan 
GRID_MIN
 the lower bounds for the grid
=-0.5 
GRID_MAX
 the upper bounds for the grid
=250.5 
GRID_BIN
the number of bins for the grid
=1000 
BANDWIDTH
the bandwidths for kernel density esimtation
=1 
hh360-9000_kdepThe CUSTOM action with label hh360-9000_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-9000_kdep
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh360-9000_kde,hh360-9000_weight 
FUNC
the function you wish to evaluate
=x*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh360-9000_uThe ACCUMULATE action with label hh360-9000_u calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-9000_u
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh360-9000_kdep 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh360-9000_nsumThe ACCUMULATE action with label hh360-9000_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-9000_nsum
scalar
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh360-9000_weight 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh360-9000The CUSTOM action with label hh360-9000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-9000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh360-9000_u,hh360-9000_nsum 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=hh360-9000 
FILE
 the file on which to write the grid
=histo360-9000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f
ff360-9000The CONVERT_TO_FES action with label ff360-9000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff360-9000
grid
the free energy surface: 
CONVERT_TO_FES
Convert a histogram to a free energy surface. This action is a shortcut. More details
 
GRID
the histogram that you would like to convert into a free energy surface (old syntax)
=hh360-9000 
TEMP
the temperature at which you are operating
=360.0
# PLUMED interprets the command:
# ff360-9000: CONVERT_TO_FES GRID=hh360-9000 TEMP=360.0
# as follows (Click the red comment above to revert to the short version of the input):
ff360-9000The CUSTOM action with label ff360-9000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff360-9000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh360-9000 
FUNC
the function you wish to evaluate
=-2.99321*log(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=ff360-9000 
FILE
 the file on which to write the grid
=fes360-9000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f

weights360-10000The REWEIGHT_TEMP_PRESS action with label weights360-10000 calculates the following quantities:
 Quantity   
 Type   
 Description  
weights360-10000
scalar
the weight to use for this frame to determine its contribution at a different temperature/pressure: 
REWEIGHT_TEMP_PRESS
Calculate weights for ensemble averages at temperatures and/or pressures different than those used in your original simulation. More details
 
TEMP
the system temperature
=400 
PRESSURE
The system pressure
=301.10704285 
REWEIGHT_TEMP
Reweighting temperature
=360.0 
REWEIGHT_PRESSURE
Reweighting pressure
=602.2140857 
ENERGY
Energy
=renergy 
VOLUME
Volume
=vol
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights360-10000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh360-10000The HISTOGRAM action with label hh360-10000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-10000
grid
the estimate of the histogram as a function of the argument that was obtained
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
... HISTOGRAM
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights360-10000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh360-10000
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
 
STRIDE
 the frequency with which to store data for averaging
=1
... HISTOGRAM
# PLUMED interprets the command:
# HISTOGRAM ...
#   ARG=refcv.morethan
#   GRID_MIN=-0.5
#   GRID_MAX=250.5
#   GRID_BIN=1000
#   BANDWIDTH=1.
#   LOGWEIGHTS=weights,weights360-10000
#   NORMALIZATION=true
#   LABEL=hh360-10000
#   CLEAR=10000
# ... HISTOGRAM
# as follows (Click the red comment above to revert to the short version of the input):
hh360-10000_wsumThe COMBINE action with label hh360-10000_wsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-10000_wsum
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=weights,weights360-10000 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh360-10000_weightThe CUSTOM action with label hh360-10000_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-10000_weight
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh360-10000_wsum 
FUNC
the function you wish to evaluate
=exp(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh360-10000_kdeThe KDE action with label hh360-10000_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-10000_kde
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
ARG
the input for this action is the scalar output from one or more other actions
=refcv.morethan 
GRID_MIN
 the lower bounds for the grid
=-0.5 
GRID_MAX
 the upper bounds for the grid
=250.5 
GRID_BIN
the number of bins for the grid
=1000 
BANDWIDTH
the bandwidths for kernel density esimtation
=1 
hh360-10000_kdepThe CUSTOM action with label hh360-10000_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-10000_kdep
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh360-10000_kde,hh360-10000_weight 
FUNC
the function you wish to evaluate
=x*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh360-10000_uThe ACCUMULATE action with label hh360-10000_u calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-10000_u
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh360-10000_kdep 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh360-10000_nsumThe ACCUMULATE action with label hh360-10000_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-10000_nsum
scalar
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh360-10000_weight 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh360-10000The CUSTOM action with label hh360-10000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh360-10000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh360-10000_u,hh360-10000_nsum 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=hh360-10000 
FILE
 the file on which to write the grid
=histo360-10000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f
ff360-10000The CONVERT_TO_FES action with label ff360-10000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff360-10000
grid
the free energy surface: 
CONVERT_TO_FES
Convert a histogram to a free energy surface. This action is a shortcut. More details
 
GRID
the histogram that you would like to convert into a free energy surface (old syntax)
=hh360-10000 
TEMP
the temperature at which you are operating
=360.0
# PLUMED interprets the command:
# ff360-10000: CONVERT_TO_FES GRID=hh360-10000 TEMP=360.0
# as follows (Click the red comment above to revert to the short version of the input):
ff360-10000The CUSTOM action with label ff360-10000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff360-10000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh360-10000 
FUNC
the function you wish to evaluate
=-2.99321*log(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=ff360-10000 
FILE
 the file on which to write the grid
=fes360-10000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f

weights370-0The REWEIGHT_TEMP_PRESS action with label weights370-0 calculates the following quantities:
 Quantity   
 Type   
 Description  
weights370-0
scalar
the weight to use for this frame to determine its contribution at a different temperature/pressure: 
REWEIGHT_TEMP_PRESS
Calculate weights for ensemble averages at temperatures and/or pressures different than those used in your original simulation. More details
 
TEMP
the system temperature
=400 
PRESSURE
The system pressure
=301.10704285 
REWEIGHT_TEMP
Reweighting temperature
=370.0 
REWEIGHT_PRESSURE
Reweighting pressure
=0.0 
ENERGY
Energy
=renergy 
VOLUME
Volume
=vol
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights370-0
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh370-0The HISTOGRAM action with label hh370-0 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-0
grid
the estimate of the histogram as a function of the argument that was obtained
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
... HISTOGRAM
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights370-0
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh370-0
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
 
STRIDE
 the frequency with which to store data for averaging
=1
... HISTOGRAM
# PLUMED interprets the command:
# HISTOGRAM ...
#   ARG=refcv.morethan
#   GRID_MIN=-0.5
#   GRID_MAX=250.5
#   GRID_BIN=1000
#   BANDWIDTH=1.
#   LOGWEIGHTS=weights,weights370-0
#   NORMALIZATION=true
#   LABEL=hh370-0
#   CLEAR=10000
# ... HISTOGRAM
# as follows (Click the red comment above to revert to the short version of the input):
hh370-0_wsumThe COMBINE action with label hh370-0_wsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-0_wsum
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=weights,weights370-0 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh370-0_weightThe CUSTOM action with label hh370-0_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-0_weight
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh370-0_wsum 
FUNC
the function you wish to evaluate
=exp(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh370-0_kdeThe KDE action with label hh370-0_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-0_kde
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
ARG
the input for this action is the scalar output from one or more other actions
=refcv.morethan 
GRID_MIN
 the lower bounds for the grid
=-0.5 
GRID_MAX
 the upper bounds for the grid
=250.5 
GRID_BIN
the number of bins for the grid
=1000 
BANDWIDTH
the bandwidths for kernel density esimtation
=1 
hh370-0_kdepThe CUSTOM action with label hh370-0_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-0_kdep
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh370-0_kde,hh370-0_weight 
FUNC
the function you wish to evaluate
=x*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh370-0_uThe ACCUMULATE action with label hh370-0_u calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-0_u
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh370-0_kdep 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh370-0_nsumThe ACCUMULATE action with label hh370-0_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-0_nsum
scalar
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh370-0_weight 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh370-0The CUSTOM action with label hh370-0 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-0
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh370-0_u,hh370-0_nsum 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=hh370-0 
FILE
 the file on which to write the grid
=histo370-0 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f
ff370-0The CONVERT_TO_FES action with label ff370-0 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff370-0
grid
the free energy surface: 
CONVERT_TO_FES
Convert a histogram to a free energy surface. This action is a shortcut. More details
 
GRID
the histogram that you would like to convert into a free energy surface (old syntax)
=hh370-0 
TEMP
the temperature at which you are operating
=370.0
# PLUMED interprets the command:
# ff370-0: CONVERT_TO_FES GRID=hh370-0 TEMP=370.0
# as follows (Click the red comment above to revert to the short version of the input):
ff370-0The CUSTOM action with label ff370-0 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff370-0
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh370-0 
FUNC
the function you wish to evaluate
=-3.07635*log(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=ff370-0 
FILE
 the file on which to write the grid
=fes370-0 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f

weights370-1000The REWEIGHT_TEMP_PRESS action with label weights370-1000 calculates the following quantities:
 Quantity   
 Type   
 Description  
weights370-1000
scalar
the weight to use for this frame to determine its contribution at a different temperature/pressure: 
REWEIGHT_TEMP_PRESS
Calculate weights for ensemble averages at temperatures and/or pressures different than those used in your original simulation. More details
 
TEMP
the system temperature
=400 
PRESSURE
The system pressure
=301.10704285 
REWEIGHT_TEMP
Reweighting temperature
=370.0 
REWEIGHT_PRESSURE
Reweighting pressure
=60.22140857 
ENERGY
Energy
=renergy 
VOLUME
Volume
=vol
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights370-1000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh370-1000The HISTOGRAM action with label hh370-1000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-1000
grid
the estimate of the histogram as a function of the argument that was obtained
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
... HISTOGRAM
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights370-1000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh370-1000
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
 
STRIDE
 the frequency with which to store data for averaging
=1
... HISTOGRAM
# PLUMED interprets the command:
# HISTOGRAM ...
#   ARG=refcv.morethan
#   GRID_MIN=-0.5
#   GRID_MAX=250.5
#   GRID_BIN=1000
#   BANDWIDTH=1.
#   LOGWEIGHTS=weights,weights370-1000
#   NORMALIZATION=true
#   LABEL=hh370-1000
#   CLEAR=10000
# ... HISTOGRAM
# as follows (Click the red comment above to revert to the short version of the input):
hh370-1000_wsumThe COMBINE action with label hh370-1000_wsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-1000_wsum
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=weights,weights370-1000 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh370-1000_weightThe CUSTOM action with label hh370-1000_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-1000_weight
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh370-1000_wsum 
FUNC
the function you wish to evaluate
=exp(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh370-1000_kdeThe KDE action with label hh370-1000_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-1000_kde
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
ARG
the input for this action is the scalar output from one or more other actions
=refcv.morethan 
GRID_MIN
 the lower bounds for the grid
=-0.5 
GRID_MAX
 the upper bounds for the grid
=250.5 
GRID_BIN
the number of bins for the grid
=1000 
BANDWIDTH
the bandwidths for kernel density esimtation
=1 
hh370-1000_kdepThe CUSTOM action with label hh370-1000_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-1000_kdep
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh370-1000_kde,hh370-1000_weight 
FUNC
the function you wish to evaluate
=x*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh370-1000_uThe ACCUMULATE action with label hh370-1000_u calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-1000_u
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh370-1000_kdep 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh370-1000_nsumThe ACCUMULATE action with label hh370-1000_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-1000_nsum
scalar
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh370-1000_weight 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh370-1000The CUSTOM action with label hh370-1000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-1000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh370-1000_u,hh370-1000_nsum 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=hh370-1000 
FILE
 the file on which to write the grid
=histo370-1000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f
ff370-1000The CONVERT_TO_FES action with label ff370-1000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff370-1000
grid
the free energy surface: 
CONVERT_TO_FES
Convert a histogram to a free energy surface. This action is a shortcut. More details
 
GRID
the histogram that you would like to convert into a free energy surface (old syntax)
=hh370-1000 
TEMP
the temperature at which you are operating
=370.0
# PLUMED interprets the command:
# ff370-1000: CONVERT_TO_FES GRID=hh370-1000 TEMP=370.0
# as follows (Click the red comment above to revert to the short version of the input):
ff370-1000The CUSTOM action with label ff370-1000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff370-1000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh370-1000 
FUNC
the function you wish to evaluate
=-3.07635*log(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=ff370-1000 
FILE
 the file on which to write the grid
=fes370-1000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f

weights370-2000The REWEIGHT_TEMP_PRESS action with label weights370-2000 calculates the following quantities:
 Quantity   
 Type   
 Description  
weights370-2000
scalar
the weight to use for this frame to determine its contribution at a different temperature/pressure: 
REWEIGHT_TEMP_PRESS
Calculate weights for ensemble averages at temperatures and/or pressures different than those used in your original simulation. More details
 
TEMP
the system temperature
=400 
PRESSURE
The system pressure
=301.10704285 
REWEIGHT_TEMP
Reweighting temperature
=370.0 
REWEIGHT_PRESSURE
Reweighting pressure
=120.44281714 
ENERGY
Energy
=renergy 
VOLUME
Volume
=vol
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights370-2000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh370-2000The HISTOGRAM action with label hh370-2000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-2000
grid
the estimate of the histogram as a function of the argument that was obtained
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
... HISTOGRAM
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights370-2000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh370-2000
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
 
STRIDE
 the frequency with which to store data for averaging
=1
... HISTOGRAM
# PLUMED interprets the command:
# HISTOGRAM ...
#   ARG=refcv.morethan
#   GRID_MIN=-0.5
#   GRID_MAX=250.5
#   GRID_BIN=1000
#   BANDWIDTH=1.
#   LOGWEIGHTS=weights,weights370-2000
#   NORMALIZATION=true
#   LABEL=hh370-2000
#   CLEAR=10000
# ... HISTOGRAM
# as follows (Click the red comment above to revert to the short version of the input):
hh370-2000_wsumThe COMBINE action with label hh370-2000_wsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-2000_wsum
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=weights,weights370-2000 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh370-2000_weightThe CUSTOM action with label hh370-2000_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-2000_weight
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh370-2000_wsum 
FUNC
the function you wish to evaluate
=exp(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh370-2000_kdeThe KDE action with label hh370-2000_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-2000_kde
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
ARG
the input for this action is the scalar output from one or more other actions
=refcv.morethan 
GRID_MIN
 the lower bounds for the grid
=-0.5 
GRID_MAX
 the upper bounds for the grid
=250.5 
GRID_BIN
the number of bins for the grid
=1000 
BANDWIDTH
the bandwidths for kernel density esimtation
=1 
hh370-2000_kdepThe CUSTOM action with label hh370-2000_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-2000_kdep
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh370-2000_kde,hh370-2000_weight 
FUNC
the function you wish to evaluate
=x*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh370-2000_uThe ACCUMULATE action with label hh370-2000_u calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-2000_u
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh370-2000_kdep 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh370-2000_nsumThe ACCUMULATE action with label hh370-2000_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-2000_nsum
scalar
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh370-2000_weight 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh370-2000The CUSTOM action with label hh370-2000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-2000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh370-2000_u,hh370-2000_nsum 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=hh370-2000 
FILE
 the file on which to write the grid
=histo370-2000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f
ff370-2000The CONVERT_TO_FES action with label ff370-2000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff370-2000
grid
the free energy surface: 
CONVERT_TO_FES
Convert a histogram to a free energy surface. This action is a shortcut. More details
 
GRID
the histogram that you would like to convert into a free energy surface (old syntax)
=hh370-2000 
TEMP
the temperature at which you are operating
=370.0
# PLUMED interprets the command:
# ff370-2000: CONVERT_TO_FES GRID=hh370-2000 TEMP=370.0
# as follows (Click the red comment above to revert to the short version of the input):
ff370-2000The CUSTOM action with label ff370-2000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff370-2000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh370-2000 
FUNC
the function you wish to evaluate
=-3.07635*log(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=ff370-2000 
FILE
 the file on which to write the grid
=fes370-2000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f

weights370-3000The REWEIGHT_TEMP_PRESS action with label weights370-3000 calculates the following quantities:
 Quantity   
 Type   
 Description  
weights370-3000
scalar
the weight to use for this frame to determine its contribution at a different temperature/pressure: 
REWEIGHT_TEMP_PRESS
Calculate weights for ensemble averages at temperatures and/or pressures different than those used in your original simulation. More details
 
TEMP
the system temperature
=400 
PRESSURE
The system pressure
=301.10704285 
REWEIGHT_TEMP
Reweighting temperature
=370.0 
REWEIGHT_PRESSURE
Reweighting pressure
=180.66422571 
ENERGY
Energy
=renergy 
VOLUME
Volume
=vol
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights370-3000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh370-3000The HISTOGRAM action with label hh370-3000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-3000
grid
the estimate of the histogram as a function of the argument that was obtained
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
... HISTOGRAM
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights370-3000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh370-3000
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
 
STRIDE
 the frequency with which to store data for averaging
=1
... HISTOGRAM
# PLUMED interprets the command:
# HISTOGRAM ...
#   ARG=refcv.morethan
#   GRID_MIN=-0.5
#   GRID_MAX=250.5
#   GRID_BIN=1000
#   BANDWIDTH=1.
#   LOGWEIGHTS=weights,weights370-3000
#   NORMALIZATION=true
#   LABEL=hh370-3000
#   CLEAR=10000
# ... HISTOGRAM
# as follows (Click the red comment above to revert to the short version of the input):
hh370-3000_wsumThe COMBINE action with label hh370-3000_wsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-3000_wsum
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=weights,weights370-3000 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh370-3000_weightThe CUSTOM action with label hh370-3000_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-3000_weight
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh370-3000_wsum 
FUNC
the function you wish to evaluate
=exp(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh370-3000_kdeThe KDE action with label hh370-3000_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-3000_kde
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
ARG
the input for this action is the scalar output from one or more other actions
=refcv.morethan 
GRID_MIN
 the lower bounds for the grid
=-0.5 
GRID_MAX
 the upper bounds for the grid
=250.5 
GRID_BIN
the number of bins for the grid
=1000 
BANDWIDTH
the bandwidths for kernel density esimtation
=1 
hh370-3000_kdepThe CUSTOM action with label hh370-3000_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-3000_kdep
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh370-3000_kde,hh370-3000_weight 
FUNC
the function you wish to evaluate
=x*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh370-3000_uThe ACCUMULATE action with label hh370-3000_u calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-3000_u
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh370-3000_kdep 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh370-3000_nsumThe ACCUMULATE action with label hh370-3000_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-3000_nsum
scalar
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh370-3000_weight 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh370-3000The CUSTOM action with label hh370-3000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-3000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh370-3000_u,hh370-3000_nsum 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=hh370-3000 
FILE
 the file on which to write the grid
=histo370-3000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f
ff370-3000The CONVERT_TO_FES action with label ff370-3000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff370-3000
grid
the free energy surface: 
CONVERT_TO_FES
Convert a histogram to a free energy surface. This action is a shortcut. More details
 
GRID
the histogram that you would like to convert into a free energy surface (old syntax)
=hh370-3000 
TEMP
the temperature at which you are operating
=370.0
# PLUMED interprets the command:
# ff370-3000: CONVERT_TO_FES GRID=hh370-3000 TEMP=370.0
# as follows (Click the red comment above to revert to the short version of the input):
ff370-3000The CUSTOM action with label ff370-3000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff370-3000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh370-3000 
FUNC
the function you wish to evaluate
=-3.07635*log(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=ff370-3000 
FILE
 the file on which to write the grid
=fes370-3000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f

weights370-4000The REWEIGHT_TEMP_PRESS action with label weights370-4000 calculates the following quantities:
 Quantity   
 Type   
 Description  
weights370-4000
scalar
the weight to use for this frame to determine its contribution at a different temperature/pressure: 
REWEIGHT_TEMP_PRESS
Calculate weights for ensemble averages at temperatures and/or pressures different than those used in your original simulation. More details
 
TEMP
the system temperature
=400 
PRESSURE
The system pressure
=301.10704285 
REWEIGHT_TEMP
Reweighting temperature
=370.0 
REWEIGHT_PRESSURE
Reweighting pressure
=240.88563428 
ENERGY
Energy
=renergy 
VOLUME
Volume
=vol
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights370-4000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh370-4000The HISTOGRAM action with label hh370-4000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-4000
grid
the estimate of the histogram as a function of the argument that was obtained
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
... HISTOGRAM
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights370-4000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh370-4000
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
 
STRIDE
 the frequency with which to store data for averaging
=1
... HISTOGRAM
# PLUMED interprets the command:
# HISTOGRAM ...
#   ARG=refcv.morethan
#   GRID_MIN=-0.5
#   GRID_MAX=250.5
#   GRID_BIN=1000
#   BANDWIDTH=1.
#   LOGWEIGHTS=weights,weights370-4000
#   NORMALIZATION=true
#   LABEL=hh370-4000
#   CLEAR=10000
# ... HISTOGRAM
# as follows (Click the red comment above to revert to the short version of the input):
hh370-4000_wsumThe COMBINE action with label hh370-4000_wsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-4000_wsum
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=weights,weights370-4000 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh370-4000_weightThe CUSTOM action with label hh370-4000_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-4000_weight
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh370-4000_wsum 
FUNC
the function you wish to evaluate
=exp(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh370-4000_kdeThe KDE action with label hh370-4000_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-4000_kde
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
ARG
the input for this action is the scalar output from one or more other actions
=refcv.morethan 
GRID_MIN
 the lower bounds for the grid
=-0.5 
GRID_MAX
 the upper bounds for the grid
=250.5 
GRID_BIN
the number of bins for the grid
=1000 
BANDWIDTH
the bandwidths for kernel density esimtation
=1 
hh370-4000_kdepThe CUSTOM action with label hh370-4000_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-4000_kdep
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh370-4000_kde,hh370-4000_weight 
FUNC
the function you wish to evaluate
=x*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh370-4000_uThe ACCUMULATE action with label hh370-4000_u calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-4000_u
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh370-4000_kdep 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh370-4000_nsumThe ACCUMULATE action with label hh370-4000_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-4000_nsum
scalar
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh370-4000_weight 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh370-4000The CUSTOM action with label hh370-4000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-4000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh370-4000_u,hh370-4000_nsum 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=hh370-4000 
FILE
 the file on which to write the grid
=histo370-4000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f
ff370-4000The CONVERT_TO_FES action with label ff370-4000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff370-4000
grid
the free energy surface: 
CONVERT_TO_FES
Convert a histogram to a free energy surface. This action is a shortcut. More details
 
GRID
the histogram that you would like to convert into a free energy surface (old syntax)
=hh370-4000 
TEMP
the temperature at which you are operating
=370.0
# PLUMED interprets the command:
# ff370-4000: CONVERT_TO_FES GRID=hh370-4000 TEMP=370.0
# as follows (Click the red comment above to revert to the short version of the input):
ff370-4000The CUSTOM action with label ff370-4000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff370-4000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh370-4000 
FUNC
the function you wish to evaluate
=-3.07635*log(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=ff370-4000 
FILE
 the file on which to write the grid
=fes370-4000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f

weights370-5000The REWEIGHT_TEMP_PRESS action with label weights370-5000 calculates the following quantities:
 Quantity   
 Type   
 Description  
weights370-5000
scalar
the weight to use for this frame to determine its contribution at a different temperature/pressure: 
REWEIGHT_TEMP_PRESS
Calculate weights for ensemble averages at temperatures and/or pressures different than those used in your original simulation. More details
 
TEMP
the system temperature
=400 
PRESSURE
The system pressure
=301.10704285 
REWEIGHT_TEMP
Reweighting temperature
=370.0 
REWEIGHT_PRESSURE
Reweighting pressure
=301.10704285 
ENERGY
Energy
=renergy 
VOLUME
Volume
=vol
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights370-5000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh370-5000The HISTOGRAM action with label hh370-5000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-5000
grid
the estimate of the histogram as a function of the argument that was obtained
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
... HISTOGRAM
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights370-5000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh370-5000
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
 
STRIDE
 the frequency with which to store data for averaging
=1
... HISTOGRAM
# PLUMED interprets the command:
# HISTOGRAM ...
#   ARG=refcv.morethan
#   GRID_MIN=-0.5
#   GRID_MAX=250.5
#   GRID_BIN=1000
#   BANDWIDTH=1.
#   LOGWEIGHTS=weights,weights370-5000
#   NORMALIZATION=true
#   LABEL=hh370-5000
#   CLEAR=10000
# ... HISTOGRAM
# as follows (Click the red comment above to revert to the short version of the input):
hh370-5000_wsumThe COMBINE action with label hh370-5000_wsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-5000_wsum
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=weights,weights370-5000 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh370-5000_weightThe CUSTOM action with label hh370-5000_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-5000_weight
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh370-5000_wsum 
FUNC
the function you wish to evaluate
=exp(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh370-5000_kdeThe KDE action with label hh370-5000_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-5000_kde
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
ARG
the input for this action is the scalar output from one or more other actions
=refcv.morethan 
GRID_MIN
 the lower bounds for the grid
=-0.5 
GRID_MAX
 the upper bounds for the grid
=250.5 
GRID_BIN
the number of bins for the grid
=1000 
BANDWIDTH
the bandwidths for kernel density esimtation
=1 
hh370-5000_kdepThe CUSTOM action with label hh370-5000_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-5000_kdep
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh370-5000_kde,hh370-5000_weight 
FUNC
the function you wish to evaluate
=x*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh370-5000_uThe ACCUMULATE action with label hh370-5000_u calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-5000_u
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh370-5000_kdep 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh370-5000_nsumThe ACCUMULATE action with label hh370-5000_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-5000_nsum
scalar
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh370-5000_weight 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh370-5000The CUSTOM action with label hh370-5000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-5000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh370-5000_u,hh370-5000_nsum 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=hh370-5000 
FILE
 the file on which to write the grid
=histo370-5000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f
ff370-5000The CONVERT_TO_FES action with label ff370-5000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff370-5000
grid
the free energy surface: 
CONVERT_TO_FES
Convert a histogram to a free energy surface. This action is a shortcut. More details
 
GRID
the histogram that you would like to convert into a free energy surface (old syntax)
=hh370-5000 
TEMP
the temperature at which you are operating
=370.0
# PLUMED interprets the command:
# ff370-5000: CONVERT_TO_FES GRID=hh370-5000 TEMP=370.0
# as follows (Click the red comment above to revert to the short version of the input):
ff370-5000The CUSTOM action with label ff370-5000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff370-5000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh370-5000 
FUNC
the function you wish to evaluate
=-3.07635*log(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=ff370-5000 
FILE
 the file on which to write the grid
=fes370-5000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f

weights370-6000The REWEIGHT_TEMP_PRESS action with label weights370-6000 calculates the following quantities:
 Quantity   
 Type   
 Description  
weights370-6000
scalar
the weight to use for this frame to determine its contribution at a different temperature/pressure: 
REWEIGHT_TEMP_PRESS
Calculate weights for ensemble averages at temperatures and/or pressures different than those used in your original simulation. More details
 
TEMP
the system temperature
=400 
PRESSURE
The system pressure
=301.10704285 
REWEIGHT_TEMP
Reweighting temperature
=370.0 
REWEIGHT_PRESSURE
Reweighting pressure
=361.32845142 
ENERGY
Energy
=renergy 
VOLUME
Volume
=vol
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights370-6000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh370-6000The HISTOGRAM action with label hh370-6000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-6000
grid
the estimate of the histogram as a function of the argument that was obtained
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
... HISTOGRAM
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights370-6000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh370-6000
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
 
STRIDE
 the frequency with which to store data for averaging
=1
... HISTOGRAM
# PLUMED interprets the command:
# HISTOGRAM ...
#   ARG=refcv.morethan
#   GRID_MIN=-0.5
#   GRID_MAX=250.5
#   GRID_BIN=1000
#   BANDWIDTH=1.
#   LOGWEIGHTS=weights,weights370-6000
#   NORMALIZATION=true
#   LABEL=hh370-6000
#   CLEAR=10000
# ... HISTOGRAM
# as follows (Click the red comment above to revert to the short version of the input):
hh370-6000_wsumThe COMBINE action with label hh370-6000_wsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-6000_wsum
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=weights,weights370-6000 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh370-6000_weightThe CUSTOM action with label hh370-6000_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-6000_weight
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh370-6000_wsum 
FUNC
the function you wish to evaluate
=exp(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh370-6000_kdeThe KDE action with label hh370-6000_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-6000_kde
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
ARG
the input for this action is the scalar output from one or more other actions
=refcv.morethan 
GRID_MIN
 the lower bounds for the grid
=-0.5 
GRID_MAX
 the upper bounds for the grid
=250.5 
GRID_BIN
the number of bins for the grid
=1000 
BANDWIDTH
the bandwidths for kernel density esimtation
=1 
hh370-6000_kdepThe CUSTOM action with label hh370-6000_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-6000_kdep
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh370-6000_kde,hh370-6000_weight 
FUNC
the function you wish to evaluate
=x*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh370-6000_uThe ACCUMULATE action with label hh370-6000_u calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-6000_u
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh370-6000_kdep 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh370-6000_nsumThe ACCUMULATE action with label hh370-6000_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-6000_nsum
scalar
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh370-6000_weight 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh370-6000The CUSTOM action with label hh370-6000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-6000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh370-6000_u,hh370-6000_nsum 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=hh370-6000 
FILE
 the file on which to write the grid
=histo370-6000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f
ff370-6000The CONVERT_TO_FES action with label ff370-6000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff370-6000
grid
the free energy surface: 
CONVERT_TO_FES
Convert a histogram to a free energy surface. This action is a shortcut. More details
 
GRID
the histogram that you would like to convert into a free energy surface (old syntax)
=hh370-6000 
TEMP
the temperature at which you are operating
=370.0
# PLUMED interprets the command:
# ff370-6000: CONVERT_TO_FES GRID=hh370-6000 TEMP=370.0
# as follows (Click the red comment above to revert to the short version of the input):
ff370-6000The CUSTOM action with label ff370-6000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff370-6000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh370-6000 
FUNC
the function you wish to evaluate
=-3.07635*log(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=ff370-6000 
FILE
 the file on which to write the grid
=fes370-6000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f

weights370-7000The REWEIGHT_TEMP_PRESS action with label weights370-7000 calculates the following quantities:
 Quantity   
 Type   
 Description  
weights370-7000
scalar
the weight to use for this frame to determine its contribution at a different temperature/pressure: 
REWEIGHT_TEMP_PRESS
Calculate weights for ensemble averages at temperatures and/or pressures different than those used in your original simulation. More details
 
TEMP
the system temperature
=400 
PRESSURE
The system pressure
=301.10704285 
REWEIGHT_TEMP
Reweighting temperature
=370.0 
REWEIGHT_PRESSURE
Reweighting pressure
=421.54985999 
ENERGY
Energy
=renergy 
VOLUME
Volume
=vol
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights370-7000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh370-7000The HISTOGRAM action with label hh370-7000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-7000
grid
the estimate of the histogram as a function of the argument that was obtained
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
... HISTOGRAM
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights370-7000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh370-7000
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
 
STRIDE
 the frequency with which to store data for averaging
=1
... HISTOGRAM
# PLUMED interprets the command:
# HISTOGRAM ...
#   ARG=refcv.morethan
#   GRID_MIN=-0.5
#   GRID_MAX=250.5
#   GRID_BIN=1000
#   BANDWIDTH=1.
#   LOGWEIGHTS=weights,weights370-7000
#   NORMALIZATION=true
#   LABEL=hh370-7000
#   CLEAR=10000
# ... HISTOGRAM
# as follows (Click the red comment above to revert to the short version of the input):
hh370-7000_wsumThe COMBINE action with label hh370-7000_wsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-7000_wsum
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=weights,weights370-7000 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh370-7000_weightThe CUSTOM action with label hh370-7000_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-7000_weight
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh370-7000_wsum 
FUNC
the function you wish to evaluate
=exp(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh370-7000_kdeThe KDE action with label hh370-7000_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-7000_kde
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
ARG
the input for this action is the scalar output from one or more other actions
=refcv.morethan 
GRID_MIN
 the lower bounds for the grid
=-0.5 
GRID_MAX
 the upper bounds for the grid
=250.5 
GRID_BIN
the number of bins for the grid
=1000 
BANDWIDTH
the bandwidths for kernel density esimtation
=1 
hh370-7000_kdepThe CUSTOM action with label hh370-7000_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-7000_kdep
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh370-7000_kde,hh370-7000_weight 
FUNC
the function you wish to evaluate
=x*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh370-7000_uThe ACCUMULATE action with label hh370-7000_u calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-7000_u
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh370-7000_kdep 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh370-7000_nsumThe ACCUMULATE action with label hh370-7000_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-7000_nsum
scalar
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh370-7000_weight 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh370-7000The CUSTOM action with label hh370-7000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-7000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh370-7000_u,hh370-7000_nsum 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=hh370-7000 
FILE
 the file on which to write the grid
=histo370-7000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f
ff370-7000The CONVERT_TO_FES action with label ff370-7000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff370-7000
grid
the free energy surface: 
CONVERT_TO_FES
Convert a histogram to a free energy surface. This action is a shortcut. More details
 
GRID
the histogram that you would like to convert into a free energy surface (old syntax)
=hh370-7000 
TEMP
the temperature at which you are operating
=370.0
# PLUMED interprets the command:
# ff370-7000: CONVERT_TO_FES GRID=hh370-7000 TEMP=370.0
# as follows (Click the red comment above to revert to the short version of the input):
ff370-7000The CUSTOM action with label ff370-7000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff370-7000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh370-7000 
FUNC
the function you wish to evaluate
=-3.07635*log(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=ff370-7000 
FILE
 the file on which to write the grid
=fes370-7000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f

weights370-8000The REWEIGHT_TEMP_PRESS action with label weights370-8000 calculates the following quantities:
 Quantity   
 Type   
 Description  
weights370-8000
scalar
the weight to use for this frame to determine its contribution at a different temperature/pressure: 
REWEIGHT_TEMP_PRESS
Calculate weights for ensemble averages at temperatures and/or pressures different than those used in your original simulation. More details
 
TEMP
the system temperature
=400 
PRESSURE
The system pressure
=301.10704285 
REWEIGHT_TEMP
Reweighting temperature
=370.0 
REWEIGHT_PRESSURE
Reweighting pressure
=481.77126856 
ENERGY
Energy
=renergy 
VOLUME
Volume
=vol
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights370-8000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh370-8000The HISTOGRAM action with label hh370-8000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-8000
grid
the estimate of the histogram as a function of the argument that was obtained
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
... HISTOGRAM
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights370-8000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh370-8000
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
 
STRIDE
 the frequency with which to store data for averaging
=1
... HISTOGRAM
# PLUMED interprets the command:
# HISTOGRAM ...
#   ARG=refcv.morethan
#   GRID_MIN=-0.5
#   GRID_MAX=250.5
#   GRID_BIN=1000
#   BANDWIDTH=1.
#   LOGWEIGHTS=weights,weights370-8000
#   NORMALIZATION=true
#   LABEL=hh370-8000
#   CLEAR=10000
# ... HISTOGRAM
# as follows (Click the red comment above to revert to the short version of the input):
hh370-8000_wsumThe COMBINE action with label hh370-8000_wsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-8000_wsum
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=weights,weights370-8000 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh370-8000_weightThe CUSTOM action with label hh370-8000_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-8000_weight
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh370-8000_wsum 
FUNC
the function you wish to evaluate
=exp(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh370-8000_kdeThe KDE action with label hh370-8000_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-8000_kde
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
ARG
the input for this action is the scalar output from one or more other actions
=refcv.morethan 
GRID_MIN
 the lower bounds for the grid
=-0.5 
GRID_MAX
 the upper bounds for the grid
=250.5 
GRID_BIN
the number of bins for the grid
=1000 
BANDWIDTH
the bandwidths for kernel density esimtation
=1 
hh370-8000_kdepThe CUSTOM action with label hh370-8000_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-8000_kdep
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh370-8000_kde,hh370-8000_weight 
FUNC
the function you wish to evaluate
=x*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh370-8000_uThe ACCUMULATE action with label hh370-8000_u calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-8000_u
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh370-8000_kdep 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh370-8000_nsumThe ACCUMULATE action with label hh370-8000_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-8000_nsum
scalar
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh370-8000_weight 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh370-8000The CUSTOM action with label hh370-8000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-8000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh370-8000_u,hh370-8000_nsum 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=hh370-8000 
FILE
 the file on which to write the grid
=histo370-8000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f
ff370-8000The CONVERT_TO_FES action with label ff370-8000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff370-8000
grid
the free energy surface: 
CONVERT_TO_FES
Convert a histogram to a free energy surface. This action is a shortcut. More details
 
GRID
the histogram that you would like to convert into a free energy surface (old syntax)
=hh370-8000 
TEMP
the temperature at which you are operating
=370.0
# PLUMED interprets the command:
# ff370-8000: CONVERT_TO_FES GRID=hh370-8000 TEMP=370.0
# as follows (Click the red comment above to revert to the short version of the input):
ff370-8000The CUSTOM action with label ff370-8000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff370-8000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh370-8000 
FUNC
the function you wish to evaluate
=-3.07635*log(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=ff370-8000 
FILE
 the file on which to write the grid
=fes370-8000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f

weights370-9000The REWEIGHT_TEMP_PRESS action with label weights370-9000 calculates the following quantities:
 Quantity   
 Type   
 Description  
weights370-9000
scalar
the weight to use for this frame to determine its contribution at a different temperature/pressure: 
REWEIGHT_TEMP_PRESS
Calculate weights for ensemble averages at temperatures and/or pressures different than those used in your original simulation. More details
 
TEMP
the system temperature
=400 
PRESSURE
The system pressure
=301.10704285 
REWEIGHT_TEMP
Reweighting temperature
=370.0 
REWEIGHT_PRESSURE
Reweighting pressure
=541.9926771300001 
ENERGY
Energy
=renergy 
VOLUME
Volume
=vol
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights370-9000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh370-9000The HISTOGRAM action with label hh370-9000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-9000
grid
the estimate of the histogram as a function of the argument that was obtained
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
... HISTOGRAM
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights370-9000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh370-9000
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
 
STRIDE
 the frequency with which to store data for averaging
=1
... HISTOGRAM
# PLUMED interprets the command:
# HISTOGRAM ...
#   ARG=refcv.morethan
#   GRID_MIN=-0.5
#   GRID_MAX=250.5
#   GRID_BIN=1000
#   BANDWIDTH=1.
#   LOGWEIGHTS=weights,weights370-9000
#   NORMALIZATION=true
#   LABEL=hh370-9000
#   CLEAR=10000
# ... HISTOGRAM
# as follows (Click the red comment above to revert to the short version of the input):
hh370-9000_wsumThe COMBINE action with label hh370-9000_wsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-9000_wsum
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=weights,weights370-9000 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh370-9000_weightThe CUSTOM action with label hh370-9000_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-9000_weight
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh370-9000_wsum 
FUNC
the function you wish to evaluate
=exp(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh370-9000_kdeThe KDE action with label hh370-9000_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-9000_kde
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
ARG
the input for this action is the scalar output from one or more other actions
=refcv.morethan 
GRID_MIN
 the lower bounds for the grid
=-0.5 
GRID_MAX
 the upper bounds for the grid
=250.5 
GRID_BIN
the number of bins for the grid
=1000 
BANDWIDTH
the bandwidths for kernel density esimtation
=1 
hh370-9000_kdepThe CUSTOM action with label hh370-9000_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-9000_kdep
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh370-9000_kde,hh370-9000_weight 
FUNC
the function you wish to evaluate
=x*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh370-9000_uThe ACCUMULATE action with label hh370-9000_u calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-9000_u
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh370-9000_kdep 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh370-9000_nsumThe ACCUMULATE action with label hh370-9000_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-9000_nsum
scalar
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh370-9000_weight 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh370-9000The CUSTOM action with label hh370-9000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-9000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh370-9000_u,hh370-9000_nsum 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=hh370-9000 
FILE
 the file on which to write the grid
=histo370-9000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f
ff370-9000The CONVERT_TO_FES action with label ff370-9000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff370-9000
grid
the free energy surface: 
CONVERT_TO_FES
Convert a histogram to a free energy surface. This action is a shortcut. More details
 
GRID
the histogram that you would like to convert into a free energy surface (old syntax)
=hh370-9000 
TEMP
the temperature at which you are operating
=370.0
# PLUMED interprets the command:
# ff370-9000: CONVERT_TO_FES GRID=hh370-9000 TEMP=370.0
# as follows (Click the red comment above to revert to the short version of the input):
ff370-9000The CUSTOM action with label ff370-9000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff370-9000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh370-9000 
FUNC
the function you wish to evaluate
=-3.07635*log(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=ff370-9000 
FILE
 the file on which to write the grid
=fes370-9000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f

weights370-10000The REWEIGHT_TEMP_PRESS action with label weights370-10000 calculates the following quantities:
 Quantity   
 Type   
 Description  
weights370-10000
scalar
the weight to use for this frame to determine its contribution at a different temperature/pressure: 
REWEIGHT_TEMP_PRESS
Calculate weights for ensemble averages at temperatures and/or pressures different than those used in your original simulation. More details
 
TEMP
the system temperature
=400 
PRESSURE
The system pressure
=301.10704285 
REWEIGHT_TEMP
Reweighting temperature
=370.0 
REWEIGHT_PRESSURE
Reweighting pressure
=602.2140857 
ENERGY
Energy
=renergy 
VOLUME
Volume
=vol
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights370-10000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh370-10000The HISTOGRAM action with label hh370-10000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-10000
grid
the estimate of the histogram as a function of the argument that was obtained
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
... HISTOGRAM
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights370-10000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh370-10000
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
 
STRIDE
 the frequency with which to store data for averaging
=1
... HISTOGRAM
# PLUMED interprets the command:
# HISTOGRAM ...
#   ARG=refcv.morethan
#   GRID_MIN=-0.5
#   GRID_MAX=250.5
#   GRID_BIN=1000
#   BANDWIDTH=1.
#   LOGWEIGHTS=weights,weights370-10000
#   NORMALIZATION=true
#   LABEL=hh370-10000
#   CLEAR=10000
# ... HISTOGRAM
# as follows (Click the red comment above to revert to the short version of the input):
hh370-10000_wsumThe COMBINE action with label hh370-10000_wsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-10000_wsum
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=weights,weights370-10000 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh370-10000_weightThe CUSTOM action with label hh370-10000_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-10000_weight
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh370-10000_wsum 
FUNC
the function you wish to evaluate
=exp(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh370-10000_kdeThe KDE action with label hh370-10000_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-10000_kde
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
ARG
the input for this action is the scalar output from one or more other actions
=refcv.morethan 
GRID_MIN
 the lower bounds for the grid
=-0.5 
GRID_MAX
 the upper bounds for the grid
=250.5 
GRID_BIN
the number of bins for the grid
=1000 
BANDWIDTH
the bandwidths for kernel density esimtation
=1 
hh370-10000_kdepThe CUSTOM action with label hh370-10000_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-10000_kdep
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh370-10000_kde,hh370-10000_weight 
FUNC
the function you wish to evaluate
=x*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh370-10000_uThe ACCUMULATE action with label hh370-10000_u calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-10000_u
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh370-10000_kdep 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh370-10000_nsumThe ACCUMULATE action with label hh370-10000_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-10000_nsum
scalar
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh370-10000_weight 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh370-10000The CUSTOM action with label hh370-10000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh370-10000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh370-10000_u,hh370-10000_nsum 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=hh370-10000 
FILE
 the file on which to write the grid
=histo370-10000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f
ff370-10000The CONVERT_TO_FES action with label ff370-10000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff370-10000
grid
the free energy surface: 
CONVERT_TO_FES
Convert a histogram to a free energy surface. This action is a shortcut. More details
 
GRID
the histogram that you would like to convert into a free energy surface (old syntax)
=hh370-10000 
TEMP
the temperature at which you are operating
=370.0
# PLUMED interprets the command:
# ff370-10000: CONVERT_TO_FES GRID=hh370-10000 TEMP=370.0
# as follows (Click the red comment above to revert to the short version of the input):
ff370-10000The CUSTOM action with label ff370-10000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff370-10000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh370-10000 
FUNC
the function you wish to evaluate
=-3.07635*log(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=ff370-10000 
FILE
 the file on which to write the grid
=fes370-10000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f

weights380-0The REWEIGHT_TEMP_PRESS action with label weights380-0 calculates the following quantities:
 Quantity   
 Type   
 Description  
weights380-0
scalar
the weight to use for this frame to determine its contribution at a different temperature/pressure: 
REWEIGHT_TEMP_PRESS
Calculate weights for ensemble averages at temperatures and/or pressures different than those used in your original simulation. More details
 
TEMP
the system temperature
=400 
PRESSURE
The system pressure
=301.10704285 
REWEIGHT_TEMP
Reweighting temperature
=380.0 
REWEIGHT_PRESSURE
Reweighting pressure
=0.0 
ENERGY
Energy
=renergy 
VOLUME
Volume
=vol
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights380-0
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh380-0The HISTOGRAM action with label hh380-0 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh380-0
grid
the estimate of the histogram as a function of the argument that was obtained
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
... HISTOGRAM
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights380-0
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh380-0
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
 
STRIDE
 the frequency with which to store data for averaging
=1
... HISTOGRAM
# PLUMED interprets the command:
# HISTOGRAM ...
#   ARG=refcv.morethan
#   GRID_MIN=-0.5
#   GRID_MAX=250.5
#   GRID_BIN=1000
#   BANDWIDTH=1.
#   LOGWEIGHTS=weights,weights380-0
#   NORMALIZATION=true
#   LABEL=hh380-0
#   CLEAR=10000
# ... HISTOGRAM
# as follows (Click the red comment above to revert to the short version of the input):
hh380-0_wsumThe COMBINE action with label hh380-0_wsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh380-0_wsum
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=weights,weights380-0 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh380-0_weightThe CUSTOM action with label hh380-0_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
hh380-0_weight
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh380-0_wsum 
FUNC
the function you wish to evaluate
=exp(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh380-0_kdeThe KDE action with label hh380-0_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
hh380-0_kde
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
ARG
the input for this action is the scalar output from one or more other actions
=refcv.morethan 
GRID_MIN
 the lower bounds for the grid
=-0.5 
GRID_MAX
 the upper bounds for the grid
=250.5 
GRID_BIN
the number of bins for the grid
=1000 
BANDWIDTH
the bandwidths for kernel density esimtation
=1 
hh380-0_kdepThe CUSTOM action with label hh380-0_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
hh380-0_kdep
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh380-0_kde,hh380-0_weight 
FUNC
the function you wish to evaluate
=x*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh380-0_uThe ACCUMULATE action with label hh380-0_u calculates the following quantities:
 Quantity   
 Type   
 Description  
hh380-0_u
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh380-0_kdep 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh380-0_nsumThe ACCUMULATE action with label hh380-0_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh380-0_nsum
scalar
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh380-0_weight 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh380-0The CUSTOM action with label hh380-0 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh380-0
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh380-0_u,hh380-0_nsum 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=hh380-0 
FILE
 the file on which to write the grid
=histo380-0 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f
ff380-0The CONVERT_TO_FES action with label ff380-0 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff380-0
grid
the free energy surface: 
CONVERT_TO_FES
Convert a histogram to a free energy surface. This action is a shortcut. More details
 
GRID
the histogram that you would like to convert into a free energy surface (old syntax)
=hh380-0 
TEMP
the temperature at which you are operating
=380.0
# PLUMED interprets the command:
# ff380-0: CONVERT_TO_FES GRID=hh380-0 TEMP=380.0
# as follows (Click the red comment above to revert to the short version of the input):
ff380-0The CUSTOM action with label ff380-0 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff380-0
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh380-0 
FUNC
the function you wish to evaluate
=-3.1595*log(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=ff380-0 
FILE
 the file on which to write the grid
=fes380-0 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f

weights380-1000The REWEIGHT_TEMP_PRESS action with label weights380-1000 calculates the following quantities:
 Quantity   
 Type   
 Description  
weights380-1000
scalar
the weight to use for this frame to determine its contribution at a different temperature/pressure: 
REWEIGHT_TEMP_PRESS
Calculate weights for ensemble averages at temperatures and/or pressures different than those used in your original simulation. More details
 
TEMP
the system temperature
=400 
PRESSURE
The system pressure
=301.10704285 
REWEIGHT_TEMP
Reweighting temperature
=380.0 
REWEIGHT_PRESSURE
Reweighting pressure
=60.22140857 
ENERGY
Energy
=renergy 
VOLUME
Volume
=vol
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights380-1000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh380-1000The HISTOGRAM action with label hh380-1000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh380-1000
grid
the estimate of the histogram as a function of the argument that was obtained
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
... HISTOGRAM
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights380-1000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh380-1000
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
 
STRIDE
 the frequency with which to store data for averaging
=1
... HISTOGRAM
# PLUMED interprets the command:
# HISTOGRAM ...
#   ARG=refcv.morethan
#   GRID_MIN=-0.5
#   GRID_MAX=250.5
#   GRID_BIN=1000
#   BANDWIDTH=1.
#   LOGWEIGHTS=weights,weights380-1000
#   NORMALIZATION=true
#   LABEL=hh380-1000
#   CLEAR=10000
# ... HISTOGRAM
# as follows (Click the red comment above to revert to the short version of the input):
hh380-1000_wsumThe COMBINE action with label hh380-1000_wsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh380-1000_wsum
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=weights,weights380-1000 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh380-1000_weightThe CUSTOM action with label hh380-1000_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
hh380-1000_weight
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh380-1000_wsum 
FUNC
the function you wish to evaluate
=exp(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh380-1000_kdeThe KDE action with label hh380-1000_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
hh380-1000_kde
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
ARG
the input for this action is the scalar output from one or more other actions
=refcv.morethan 
GRID_MIN
 the lower bounds for the grid
=-0.5 
GRID_MAX
 the upper bounds for the grid
=250.5 
GRID_BIN
the number of bins for the grid
=1000 
BANDWIDTH
the bandwidths for kernel density esimtation
=1 
hh380-1000_kdepThe CUSTOM action with label hh380-1000_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
hh380-1000_kdep
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh380-1000_kde,hh380-1000_weight 
FUNC
the function you wish to evaluate
=x*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh380-1000_uThe ACCUMULATE action with label hh380-1000_u calculates the following quantities:
 Quantity   
 Type   
 Description  
hh380-1000_u
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh380-1000_kdep 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh380-1000_nsumThe ACCUMULATE action with label hh380-1000_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh380-1000_nsum
scalar
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh380-1000_weight 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh380-1000The CUSTOM action with label hh380-1000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh380-1000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh380-1000_u,hh380-1000_nsum 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=hh380-1000 
FILE
 the file on which to write the grid
=histo380-1000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f
ff380-1000The CONVERT_TO_FES action with label ff380-1000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff380-1000
grid
the free energy surface: 
CONVERT_TO_FES
Convert a histogram to a free energy surface. This action is a shortcut. More details
 
GRID
the histogram that you would like to convert into a free energy surface (old syntax)
=hh380-1000 
TEMP
the temperature at which you are operating
=380.0
# PLUMED interprets the command:
# ff380-1000: CONVERT_TO_FES GRID=hh380-1000 TEMP=380.0
# as follows (Click the red comment above to revert to the short version of the input):
ff380-1000The CUSTOM action with label ff380-1000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff380-1000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh380-1000 
FUNC
the function you wish to evaluate
=-3.1595*log(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=ff380-1000 
FILE
 the file on which to write the grid
=fes380-1000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f

weights380-2000The REWEIGHT_TEMP_PRESS action with label weights380-2000 calculates the following quantities:
 Quantity   
 Type   
 Description  
weights380-2000
scalar
the weight to use for this frame to determine its contribution at a different temperature/pressure: 
REWEIGHT_TEMP_PRESS
Calculate weights for ensemble averages at temperatures and/or pressures different than those used in your original simulation. More details
 
TEMP
the system temperature
=400 
PRESSURE
The system pressure
=301.10704285 
REWEIGHT_TEMP
Reweighting temperature
=380.0 
REWEIGHT_PRESSURE
Reweighting pressure
=120.44281714 
ENERGY
Energy
=renergy 
VOLUME
Volume
=vol
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights380-2000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh380-2000The HISTOGRAM action with label hh380-2000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh380-2000
grid
the estimate of the histogram as a function of the argument that was obtained
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
... HISTOGRAM
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights380-2000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh380-2000
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
 
STRIDE
 the frequency with which to store data for averaging
=1
... HISTOGRAM
# PLUMED interprets the command:
# HISTOGRAM ...
#   ARG=refcv.morethan
#   GRID_MIN=-0.5
#   GRID_MAX=250.5
#   GRID_BIN=1000
#   BANDWIDTH=1.
#   LOGWEIGHTS=weights,weights380-2000
#   NORMALIZATION=true
#   LABEL=hh380-2000
#   CLEAR=10000
# ... HISTOGRAM
# as follows (Click the red comment above to revert to the short version of the input):
hh380-2000_wsumThe COMBINE action with label hh380-2000_wsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh380-2000_wsum
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=weights,weights380-2000 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh380-2000_weightThe CUSTOM action with label hh380-2000_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
hh380-2000_weight
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh380-2000_wsum 
FUNC
the function you wish to evaluate
=exp(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh380-2000_kdeThe KDE action with label hh380-2000_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
hh380-2000_kde
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
ARG
the input for this action is the scalar output from one or more other actions
=refcv.morethan 
GRID_MIN
 the lower bounds for the grid
=-0.5 
GRID_MAX
 the upper bounds for the grid
=250.5 
GRID_BIN
the number of bins for the grid
=1000 
BANDWIDTH
the bandwidths for kernel density esimtation
=1 
hh380-2000_kdepThe CUSTOM action with label hh380-2000_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
hh380-2000_kdep
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh380-2000_kde,hh380-2000_weight 
FUNC
the function you wish to evaluate
=x*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh380-2000_uThe ACCUMULATE action with label hh380-2000_u calculates the following quantities:
 Quantity   
 Type   
 Description  
hh380-2000_u
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh380-2000_kdep 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh380-2000_nsumThe ACCUMULATE action with label hh380-2000_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh380-2000_nsum
scalar
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh380-2000_weight 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh380-2000The CUSTOM action with label hh380-2000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh380-2000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh380-2000_u,hh380-2000_nsum 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=hh380-2000 
FILE
 the file on which to write the grid
=histo380-2000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f
ff380-2000The CONVERT_TO_FES action with label ff380-2000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff380-2000
grid
the free energy surface: 
CONVERT_TO_FES
Convert a histogram to a free energy surface. This action is a shortcut. More details
 
GRID
the histogram that you would like to convert into a free energy surface (old syntax)
=hh380-2000 
TEMP
the temperature at which you are operating
=380.0
# PLUMED interprets the command:
# ff380-2000: CONVERT_TO_FES GRID=hh380-2000 TEMP=380.0
# as follows (Click the red comment above to revert to the short version of the input):
ff380-2000The CUSTOM action with label ff380-2000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff380-2000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh380-2000 
FUNC
the function you wish to evaluate
=-3.1595*log(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=ff380-2000 
FILE
 the file on which to write the grid
=fes380-2000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f

weights380-3000The REWEIGHT_TEMP_PRESS action with label weights380-3000 calculates the following quantities:
 Quantity   
 Type   
 Description  
weights380-3000
scalar
the weight to use for this frame to determine its contribution at a different temperature/pressure: 
REWEIGHT_TEMP_PRESS
Calculate weights for ensemble averages at temperatures and/or pressures different than those used in your original simulation. More details
 
TEMP
the system temperature
=400 
PRESSURE
The system pressure
=301.10704285 
REWEIGHT_TEMP
Reweighting temperature
=380.0 
REWEIGHT_PRESSURE
Reweighting pressure
=180.66422571 
ENERGY
Energy
=renergy 
VOLUME
Volume
=vol
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights380-3000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh380-3000The HISTOGRAM action with label hh380-3000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh380-3000
grid
the estimate of the histogram as a function of the argument that was obtained
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
... HISTOGRAM
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights380-3000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh380-3000
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
 
STRIDE
 the frequency with which to store data for averaging
=1
... HISTOGRAM
# PLUMED interprets the command:
# HISTOGRAM ...
#   ARG=refcv.morethan
#   GRID_MIN=-0.5
#   GRID_MAX=250.5
#   GRID_BIN=1000
#   BANDWIDTH=1.
#   LOGWEIGHTS=weights,weights380-3000
#   NORMALIZATION=true
#   LABEL=hh380-3000
#   CLEAR=10000
# ... HISTOGRAM
# as follows (Click the red comment above to revert to the short version of the input):
hh380-3000_wsumThe COMBINE action with label hh380-3000_wsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh380-3000_wsum
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=weights,weights380-3000 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh380-3000_weightThe CUSTOM action with label hh380-3000_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
hh380-3000_weight
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh380-3000_wsum 
FUNC
the function you wish to evaluate
=exp(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh380-3000_kdeThe KDE action with label hh380-3000_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
hh380-3000_kde
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
ARG
the input for this action is the scalar output from one or more other actions
=refcv.morethan 
GRID_MIN
 the lower bounds for the grid
=-0.5 
GRID_MAX
 the upper bounds for the grid
=250.5 
GRID_BIN
the number of bins for the grid
=1000 
BANDWIDTH
the bandwidths for kernel density esimtation
=1 
hh380-3000_kdepThe CUSTOM action with label hh380-3000_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
hh380-3000_kdep
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh380-3000_kde,hh380-3000_weight 
FUNC
the function you wish to evaluate
=x*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh380-3000_uThe ACCUMULATE action with label hh380-3000_u calculates the following quantities:
 Quantity   
 Type   
 Description  
hh380-3000_u
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh380-3000_kdep 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh380-3000_nsumThe ACCUMULATE action with label hh380-3000_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh380-3000_nsum
scalar
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh380-3000_weight 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh380-3000The CUSTOM action with label hh380-3000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh380-3000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh380-3000_u,hh380-3000_nsum 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=hh380-3000 
FILE
 the file on which to write the grid
=histo380-3000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f
ff380-3000The CONVERT_TO_FES action with label ff380-3000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff380-3000
grid
the free energy surface: 
CONVERT_TO_FES
Convert a histogram to a free energy surface. This action is a shortcut. More details
 
GRID
the histogram that you would like to convert into a free energy surface (old syntax)
=hh380-3000 
TEMP
the temperature at which you are operating
=380.0
# PLUMED interprets the command:
# ff380-3000: CONVERT_TO_FES GRID=hh380-3000 TEMP=380.0
# as follows (Click the red comment above to revert to the short version of the input):
ff380-3000The CUSTOM action with label ff380-3000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff380-3000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh380-3000 
FUNC
the function you wish to evaluate
=-3.1595*log(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=ff380-3000 
FILE
 the file on which to write the grid
=fes380-3000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f

weights380-4000The REWEIGHT_TEMP_PRESS action with label weights380-4000 calculates the following quantities:
 Quantity   
 Type   
 Description  
weights380-4000
scalar
the weight to use for this frame to determine its contribution at a different temperature/pressure: 
REWEIGHT_TEMP_PRESS
Calculate weights for ensemble averages at temperatures and/or pressures different than those used in your original simulation. More details
 
TEMP
the system temperature
=400 
PRESSURE
The system pressure
=301.10704285 
REWEIGHT_TEMP
Reweighting temperature
=380.0 
REWEIGHT_PRESSURE
Reweighting pressure
=240.88563428 
ENERGY
Energy
=renergy 
VOLUME
Volume
=vol
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights380-4000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh380-4000The HISTOGRAM action with label hh380-4000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh380-4000
grid
the estimate of the histogram as a function of the argument that was obtained
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
... HISTOGRAM
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights380-4000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh380-4000
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
 
STRIDE
 the frequency with which to store data for averaging
=1
... HISTOGRAM
# PLUMED interprets the command:
# HISTOGRAM ...
#   ARG=refcv.morethan
#   GRID_MIN=-0.5
#   GRID_MAX=250.5
#   GRID_BIN=1000
#   BANDWIDTH=1.
#   LOGWEIGHTS=weights,weights380-4000
#   NORMALIZATION=true
#   LABEL=hh380-4000
#   CLEAR=10000
# ... HISTOGRAM
# as follows (Click the red comment above to revert to the short version of the input):
hh380-4000_wsumThe COMBINE action with label hh380-4000_wsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh380-4000_wsum
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=weights,weights380-4000 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh380-4000_weightThe CUSTOM action with label hh380-4000_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
hh380-4000_weight
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh380-4000_wsum 
FUNC
the function you wish to evaluate
=exp(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh380-4000_kdeThe KDE action with label hh380-4000_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
hh380-4000_kde
grid
a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments: 
KDE
Create a histogram from the input scalar/vector/matrix using KDE More details
 
ARG
the input for this action is the scalar output from one or more other actions
=refcv.morethan 
GRID_MIN
 the lower bounds for the grid
=-0.5 
GRID_MAX
 the upper bounds for the grid
=250.5 
GRID_BIN
the number of bins for the grid
=1000 
BANDWIDTH
the bandwidths for kernel density esimtation
=1 
hh380-4000_kdepThe CUSTOM action with label hh380-4000_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
hh380-4000_kdep
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh380-4000_kde,hh380-4000_weight 
FUNC
the function you wish to evaluate
=x*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
hh380-4000_uThe ACCUMULATE action with label hh380-4000_u calculates the following quantities:
 Quantity   
 Type   
 Description  
hh380-4000_u
grid
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh380-4000_kdep 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh380-4000_nsumThe ACCUMULATE action with label hh380-4000_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh380-4000_nsum
scalar
a sum calculated from the time series of the input quantity: 
ACCUMULATE
Sum the elements of this value over the course of the trajectory More details
 
ARG
the input for this action is the scalar output from one or more other actions
=hh380-4000_weight 
STRIDE
 the frequency with which the data should be collected and added to the quantity being averaged
=1 
CLEAR
 the frequency with which to clear all the accumulated data
=10000 
hh380-4000The CUSTOM action with label hh380-4000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh380-4000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh380-4000_u,hh380-4000_nsum 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=hh380-4000 
FILE
 the file on which to write the grid
=histo380-4000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f
ff380-4000The CONVERT_TO_FES action with label ff380-4000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff380-4000
grid
the free energy surface: 
CONVERT_TO_FES
Convert a histogram to a free energy surface. This action is a shortcut. More details
 
GRID
the histogram that you would like to convert into a free energy surface (old syntax)
=hh380-4000 
TEMP
the temperature at which you are operating
=380.0
# PLUMED interprets the command:
# ff380-4000: CONVERT_TO_FES GRID=hh380-4000 TEMP=380.0
# as follows (Click the red comment above to revert to the short version of the input):
ff380-4000The CUSTOM action with label ff380-4000 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff380-4000
grid
the grid obtained by doing an element-wise application of an arbitrary function to the input grid: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=hh380-4000 
FUNC
the function you wish to evaluate
=-3.1595*log(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=ff380-4000 
FILE
 the file on which to write the grid
=fes380-4000 
STRIDE
 the frequency with which the grid should be output to the file
=10000 
FMT
the format that should be used to output real numbers
=%16.10f

weights380-5000The REWEIGHT_TEMP_PRESS action with label weights380-5000 calculates the following quantities:
 Quantity   
 Type   
 Description  
weights380-5000
scalar
the weight to use for this frame to determine its contribution at a different temperature/pressure: 
REWEIGHT_TEMP_PRESS
Calculate weights for ensemble averages at temperatures and/or pressures different than those used in your original simulation. More details
 
TEMP
the system temperature
=400 
PRESSURE
The system pressure
=301.10704285 
REWEIGHT_TEMP
Reweighting temperature
=380.0 
REWEIGHT_PRESSURE
Reweighting pressure
=301.10704285 
ENERGY
Energy
=renergy 
VOLUME
Volume
=vol
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights380-5000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh380-5000The HISTOGRAM action with label hh380-5000 calculates the following quantities:
 Quantity   
 Type   
 Description  
hh380-5000
grid
the estimate of the histogram as a function of the argument that was obtained
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
... HISTOGRAM
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and uses the defaults shown here. More details
 ...
  
ARG
the quantity that is being averaged
=refcv.morethan
  
GRID_MIN
 the lower bounds for the grid
=-0.5
  
GRID_MAX
 the upper bounds for the grid
=250.5
  
GRID_BIN
the number of bins for the grid
=1000
  
BANDWIDTH
the bandwidths for kernel density esimtation
=1
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights,weights380-5000
  
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=true
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh380-5000
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=10000
 
STRIDE
 the frequency with which to store data for averaging
=1
... HISTOGRAM
# PLUMED interprets the command:
# HISTOGRAM ...
#   ARG=refcv.morethan
#   GRID_MIN=-0.5
#   GRID_MAX=250.5
#   GRID_BIN=1000
#   BANDWIDTH=1.
#   LOGWEIGHTS=weights,weights380-5000
#   NORMALIZATION=true
#   LABEL=hh380-5000