PLUMED-NEST

Project ID: plumID:23.016
Source: plumed_reweight_microsw_adr_bin.dat
Originally used with PLUMED version: 2.5.3
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

#MOLINFO  STRUCTURE=adr_bin_ref.pdb

rbiasThe READ action with label rbias calculates the following quantities:
 Quantity   
 Type   
 Description  
rbias.rbias
scalar
values from the column labelled meta.rbias in the file named COLVAR: 
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
=COLVAR 
VALUES
the values to read from the file
=meta.rbias 
IGNORE_TIME
 ignore the time in the colvar file
  
rbias: 
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
=COLVAR 
VALUES
the values to read from the file
=meta.rbias 
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
tm3-tm6_1The READ action with label tm3-tm6_1 calculates the following quantities:
 Quantity   
 Type   
 Description  
tm3-tm6_1
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
=COLVAR 
VALUES
the values to read from the file
=tm3-tm6_1 
IGNORE_TIME
 ignore the time in the colvar file
 
tm3-tm6_1: 
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
=COLVAR 
VALUES
the values to read from the file
=tm3-tm6_1 
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
tm3-tm6_2The READ action with label tm3-tm6_2 calculates the following quantities:
 Quantity   
 Type   
 Description  
tm3-tm6_2
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
=COLVAR 
VALUES
the values to read from the file
=tm3-tm6_2 
IGNORE_TIME
 ignore the time in the colvar file
 
tm3-tm6_2: 
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
=COLVAR 
VALUES
the values to read from the file
=tm3-tm6_2 
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
NPxxY_iThe READ action with label NPxxY_i calculates the following quantities:
 Quantity   
 Type   
 Description  
NPxxY_i
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
=COLVAR 
VALUES
the values to read from the file
=NPxxY_i 
IGNORE_TIME
 ignore the time in the colvar file
 
NPxxY_i: 
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
=COLVAR 
VALUES
the values to read from the file
=NPxxY_i 
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
yyThe READ action with label yy calculates the following quantities:
 Quantity   
 Type   
 Description  
yy
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
=COLVAR 
VALUES
the values to read from the file
=yy 
IGNORE_TIME
 ignore the time in the colvar file
 
yy: 
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
=COLVAR 
VALUES
the values to read from the file
=yy 
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
PIF_iThe READ action with label PIF_i calculates the following quantities:
 Quantity   
 Type   
 Description  
PIF_i
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
=COLVAR 
VALUES
the values to read from the file
=PIF_i 
IGNORE_TIME
 ignore the time in the colvar file
 
PIF_i: 
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
=COLVAR 
VALUES
the values to read from the file
=PIF_i 
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
tm5The READ action with label tm5 calculates the following quantities:
 Quantity   
 Type   
 Description  
tm5
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
=COLVAR 
VALUES
the values to read from the file
=tm5 
IGNORE_TIME
 ignore the time in the colvar file
 
tm5: 
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
=COLVAR 
VALUES
the values to read from the file
=tm5 
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

biasThe REWEIGHT_METAD action with label bias calculates the following quantities:
 Quantity   
 Type   
 Description  
bias
scalar
the weight to use for this frame to negate the effect the metadynamics bias: 
REWEIGHT_METAD
Calculate the weights configurations should contribute to the histogram in a simulation in which a metadynamics bias acts upon the system. This action has hidden defaults. More details
 
TEMP
the system temperature
=310
bias: 
REWEIGHT_METAD
Calculate the weights configurations should contribute to the histogram in a simulation in which a metadynamics bias acts upon the system. This action uses the defaults shown here. More details
 
TEMP
the system temperature
=310  
ARG
 the biases that must be taken into account when reweighting
=*.rbias

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
=tm3-tm6_1
BANDWIDTH
the bandwidths for kernel density esimtation
=0.015
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=bias
LABEL
a label for the action so that its output can be referenced in the input to other actions
=histo5The HISTOGRAM action with label histo5 calculates the following quantities:
 Quantity   
 Type   
 Description  
histo5
grid
the estimate of the histogram as a function of the argument that was obtained
GRID_MIN
 the lower bounds for the grid
=0.58
GRID_MAX
 the upper bounds for the grid
=1.78
GRID_BIN
the number of bins for the grid
=150
...
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
=tm3-tm6_1
BANDWIDTH
the bandwidths for kernel density esimtation
=0.015
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=bias
LABEL
a label for the action so that its output can be referenced in the input to other actions
=histo5
GRID_MIN
 the lower bounds for the grid
=0.58
GRID_MAX
 the upper bounds for the grid
=1.78
GRID_BIN
the number of bins for the grid
=150
 
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=ndata 
STRIDE
 the frequency with which to store data for averaging
=1 
CLEAR
 the frequency with whihc to clear the data that is being averaged
=0
...
# PLUMED interprets the command:
# HISTOGRAM ...
# ARG=tm3-tm6_1
# BANDWIDTH=0.015
# LOGWEIGHTS=bias
# LABEL=histo5
# GRID_MIN=0.58
# GRID_MAX=1.78
# GRID_BIN=150
# ...
# as follows (Click the red comment above to revert to the short version of the input):
histo5_weightThe CONSTANT action with label histo5_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
histo5_weight
scalar
the constant value that was read from the plumed input: 
ONES
Create a constant vector with all elements equal to one More details
 
SIZE
the number of ones that you would like to create
=1
histo5_kdeThe KDE action with label histo5_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
histo5_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
=tm3-tm6_1 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.015 
GRID_MIN
 the lower bounds for the grid
=0.58 
GRID_MAX
 the upper bounds for the grid
=1.78 
GRID_BIN
the number of bins for the grid
=150 
histo5_kdepThe CUSTOM action with label histo5_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
histo5_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
=histo5_kde,histo5_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 
histo5_uThe ACCUMULATE action with label histo5_u calculates the following quantities:
 Quantity   
 Type   
 Description  
histo5_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
=histo5_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
=0 
histo5_nsumThe ACCUMULATE action with label histo5_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
histo5_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
=histo5_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
=0 
histo5The CUSTOM action with label histo5 calculates the following quantities:
 Quantity   
 Type   
 Description  
histo5
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
=histo5_u,histo5_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 --- 
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
=NPxxY_i
BANDWIDTH
the bandwidths for kernel density esimtation
=0.007
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=bias
LABEL
a label for the action so that its output can be referenced in the input to other actions
=histo6The HISTOGRAM action with label histo6 calculates the following quantities:
 Quantity   
 Type   
 Description  
histo6
grid
the estimate of the histogram as a function of the argument that was obtained
GRID_MIN
 the lower bounds for the grid
=0.146
GRID_MAX
 the upper bounds for the grid
=0.644
GRID_BIN
the number of bins for the grid
=150
...
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
=NPxxY_i
BANDWIDTH
the bandwidths for kernel density esimtation
=0.007
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=bias
LABEL
a label for the action so that its output can be referenced in the input to other actions
=histo6
GRID_MIN
 the lower bounds for the grid
=0.146
GRID_MAX
 the upper bounds for the grid
=0.644
GRID_BIN
the number of bins for the grid
=150
 
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=ndata 
STRIDE
 the frequency with which to store data for averaging
=1 
CLEAR
 the frequency with whihc to clear the data that is being averaged
=0
...
# PLUMED interprets the command:
# HISTOGRAM ...
# ARG=NPxxY_i
# BANDWIDTH=0.007
# LOGWEIGHTS=bias
# LABEL=histo6
# GRID_MIN=0.146
# GRID_MAX=0.644
# GRID_BIN=150
# ...
# as follows (Click the red comment above to revert to the short version of the input):
histo6_weightThe CONSTANT action with label histo6_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
histo6_weight
scalar
the constant value that was read from the plumed input: 
ONES
Create a constant vector with all elements equal to one More details
 
SIZE
the number of ones that you would like to create
=1
histo6_kdeThe KDE action with label histo6_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
histo6_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
=NPxxY_i 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.007 
GRID_MIN
 the lower bounds for the grid
=0.146 
GRID_MAX
 the upper bounds for the grid
=0.644 
GRID_BIN
the number of bins for the grid
=150 
histo6_kdepThe CUSTOM action with label histo6_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
histo6_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
=histo6_kde,histo6_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 
histo6_uThe ACCUMULATE action with label histo6_u calculates the following quantities:
 Quantity   
 Type   
 Description  
histo6_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
=histo6_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
=0 
histo6_nsumThe ACCUMULATE action with label histo6_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
histo6_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
=histo6_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
=0 
histo6The CUSTOM action with label histo6 calculates the following quantities:
 Quantity   
 Type   
 Description  
histo6
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
=histo6_u,histo6_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 --- 
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
=PIF_i
BANDWIDTH
the bandwidths for kernel density esimtation
=0.01
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=bias
LABEL
a label for the action so that its output can be referenced in the input to other actions
=histo7The HISTOGRAM action with label histo7 calculates the following quantities:
 Quantity   
 Type   
 Description  
histo7
grid
the estimate of the histogram as a function of the argument that was obtained
GRID_MIN
 the lower bounds for the grid
=0.08
GRID_MAX
 the upper bounds for the grid
=0.674
GRID_BIN
the number of bins for the grid
=150
...
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
=PIF_i
BANDWIDTH
the bandwidths for kernel density esimtation
=0.01
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=bias
LABEL
a label for the action so that its output can be referenced in the input to other actions
=histo7
GRID_MIN
 the lower bounds for the grid
=0.08
GRID_MAX
 the upper bounds for the grid
=0.674
GRID_BIN
the number of bins for the grid
=150
 
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=ndata 
STRIDE
 the frequency with which to store data for averaging
=1 
CLEAR
 the frequency with whihc to clear the data that is being averaged
=0
...
# PLUMED interprets the command:
# HISTOGRAM ...
# ARG=PIF_i
# BANDWIDTH=0.01
# LOGWEIGHTS=bias
# LABEL=histo7
# GRID_MIN=0.08
# GRID_MAX=0.674
# GRID_BIN=150
# ...
# as follows (Click the red comment above to revert to the short version of the input):
histo7_weightThe CONSTANT action with label histo7_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
histo7_weight
scalar
the constant value that was read from the plumed input: 
ONES
Create a constant vector with all elements equal to one More details
 
SIZE
the number of ones that you would like to create
=1
histo7_kdeThe KDE action with label histo7_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
histo7_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
=PIF_i 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.01 
GRID_MIN
 the lower bounds for the grid
=0.08 
GRID_MAX
 the upper bounds for the grid
=0.674 
GRID_BIN
the number of bins for the grid
=150 
histo7_kdepThe CUSTOM action with label histo7_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
histo7_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
=histo7_kde,histo7_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 
histo7_uThe ACCUMULATE action with label histo7_u calculates the following quantities:
 Quantity   
 Type   
 Description  
histo7_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
=histo7_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
=0 
histo7_nsumThe ACCUMULATE action with label histo7_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
histo7_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
=histo7_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
=0 
histo7The CUSTOM action with label histo7 calculates the following quantities:
 Quantity   
 Type   
 Description  
histo7
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
=histo7_u,histo7_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 --- 
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
=yy
BANDWIDTH
the bandwidths for kernel density esimtation
=0.03
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=bias
LABEL
a label for the action so that its output can be referenced in the input to other actions
=histo9The HISTOGRAM action with label histo9 calculates the following quantities:
 Quantity   
 Type   
 Description  
histo9
grid
the estimate of the histogram as a function of the argument that was obtained
GRID_MIN
 the lower bounds for the grid
=0.33
GRID_MAX
 the upper bounds for the grid
=1.78
GRID_BIN
the number of bins for the grid
=150
...
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
=yy
BANDWIDTH
the bandwidths for kernel density esimtation
=0.03
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=bias
LABEL
a label for the action so that its output can be referenced in the input to other actions
=histo9
GRID_MIN
 the lower bounds for the grid
=0.33
GRID_MAX
 the upper bounds for the grid
=1.78
GRID_BIN
the number of bins for the grid
=150
 
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=ndata 
STRIDE
 the frequency with which to store data for averaging
=1 
CLEAR
 the frequency with whihc to clear the data that is being averaged
=0
...
# PLUMED interprets the command:
# HISTOGRAM ...
# ARG=yy
# BANDWIDTH=0.03
# LOGWEIGHTS=bias
# LABEL=histo9
# GRID_MIN=0.33
# GRID_MAX=1.78
# GRID_BIN=150
# ...
# as follows (Click the red comment above to revert to the short version of the input):
histo9_weightThe CONSTANT action with label histo9_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
histo9_weight
scalar
the constant value that was read from the plumed input: 
ONES
Create a constant vector with all elements equal to one More details
 
SIZE
the number of ones that you would like to create
=1
histo9_kdeThe KDE action with label histo9_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
histo9_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
=yy 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.03 
GRID_MIN
 the lower bounds for the grid
=0.33 
GRID_MAX
 the upper bounds for the grid
=1.78 
GRID_BIN
the number of bins for the grid
=150 
histo9_kdepThe CUSTOM action with label histo9_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
histo9_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
=histo9_kde,histo9_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 
histo9_uThe ACCUMULATE action with label histo9_u calculates the following quantities:
 Quantity   
 Type   
 Description  
histo9_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
=histo9_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
=0 
histo9_nsumThe ACCUMULATE action with label histo9_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
histo9_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
=histo9_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
=0 
histo9The CUSTOM action with label histo9 calculates the following quantities:
 Quantity   
 Type   
 Description  
histo9
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
=histo9_u,histo9_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 --- 
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
=tm5
BANDWIDTH
the bandwidths for kernel density esimtation
=0.03
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=bias
LABEL
a label for the action so that its output can be referenced in the input to other actions
=histo10The HISTOGRAM action with label histo10 calculates the following quantities:
 Quantity   
 Type   
 Description  
histo10
grid
the estimate of the histogram as a function of the argument that was obtained
GRID_MIN
 the lower bounds for the grid
=0.73
GRID_MAX
 the upper bounds for the grid
=1.66
GRID_BIN
the number of bins for the grid
=150
...
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
=tm5
BANDWIDTH
the bandwidths for kernel density esimtation
=0.03
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=bias
LABEL
a label for the action so that its output can be referenced in the input to other actions
=histo10
GRID_MIN
 the lower bounds for the grid
=0.73
GRID_MAX
 the upper bounds for the grid
=1.66
GRID_BIN
the number of bins for the grid
=150
 
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=ndata 
STRIDE
 the frequency with which to store data for averaging
=1 
CLEAR
 the frequency with whihc to clear the data that is being averaged
=0
...
# PLUMED interprets the command:
# HISTOGRAM ...
# ARG=tm5
# BANDWIDTH=0.03
# LOGWEIGHTS=bias
# LABEL=histo10
# GRID_MIN=0.73
# GRID_MAX=1.66
# GRID_BIN=150
# ...
# as follows (Click the red comment above to revert to the short version of the input):
histo10_weightThe CONSTANT action with label histo10_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
histo10_weight
scalar
the constant value that was read from the plumed input: 
ONES
Create a constant vector with all elements equal to one More details
 
SIZE
the number of ones that you would like to create
=1
histo10_kdeThe KDE action with label histo10_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
histo10_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
=tm5 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.03 
GRID_MIN
 the lower bounds for the grid
=0.73 
GRID_MAX
 the upper bounds for the grid
=1.66 
GRID_BIN
the number of bins for the grid
=150 
histo10_kdepThe CUSTOM action with label histo10_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
histo10_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
=histo10_kde,histo10_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 
histo10_uThe ACCUMULATE action with label histo10_u calculates the following quantities:
 Quantity   
 Type   
 Description  
histo10_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
=histo10_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
=0 
histo10_nsumThe ACCUMULATE action with label histo10_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
histo10_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
=histo10_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
=0 
histo10The CUSTOM action with label histo10 calculates the following quantities:
 Quantity   
 Type   
 Description  
histo10
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
=histo10_u,histo10_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 --- 
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
=tm3-tm6_2
BANDWIDTH
the bandwidths for kernel density esimtation
=0.015
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=bias
LABEL
a label for the action so that its output can be referenced in the input to other actions
=histo13The HISTOGRAM action with label histo13 calculates the following quantities:
 Quantity   
 Type   
 Description  
histo13
grid
the estimate of the histogram as a function of the argument that was obtained
GRID_MIN
 the lower bounds for the grid
=0.88
GRID_MAX
 the upper bounds for the grid
=2.19
GRID_BIN
the number of bins for the grid
=150

...
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
=tm3-tm6_2
BANDWIDTH
the bandwidths for kernel density esimtation
=0.015
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=bias
LABEL
a label for the action so that its output can be referenced in the input to other actions
=histo13
GRID_MIN
 the lower bounds for the grid
=0.88
GRID_MAX
 the upper bounds for the grid
=2.19
GRID_BIN
the number of bins for the grid
=150

 
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=ndata 
STRIDE
 the frequency with which to store data for averaging
=1 
CLEAR
 the frequency with whihc to clear the data that is being averaged
=0
...
# PLUMED interprets the command:
# HISTOGRAM ...
# ARG=tm3-tm6_2
# BANDWIDTH=0.015
# LOGWEIGHTS=bias
# LABEL=histo13
# GRID_MIN=0.88
# GRID_MAX=2.19
# GRID_BIN=150
# 
# ...
# as follows (Click the red comment above to revert to the short version of the input):
histo13_weightThe CONSTANT action with label histo13_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
histo13_weight
scalar
the constant value that was read from the plumed input: 
ONES
Create a constant vector with all elements equal to one More details
 
SIZE
the number of ones that you would like to create
=1
histo13_kdeThe KDE action with label histo13_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
histo13_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
=tm3-tm6_2 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.015 
GRID_MIN
 the lower bounds for the grid
=0.88 
GRID_MAX
 the upper bounds for the grid
=2.19 
GRID_BIN
the number of bins for the grid
=150 
histo13_kdepThe CUSTOM action with label histo13_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
histo13_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
=histo13_kde,histo13_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 
histo13_uThe ACCUMULATE action with label histo13_u calculates the following quantities:
 Quantity   
 Type   
 Description  
histo13_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
=histo13_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
=0 
histo13_nsumThe ACCUMULATE action with label histo13_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
histo13_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
=histo13_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
=0 
histo13The CUSTOM action with label histo13 calculates the following quantities:
 Quantity   
 Type   
 Description  
histo13
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
=histo13_u,histo13_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 --- 

ff5The CONVERT_TO_FES action with label ff5 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff5
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)
=histo5 
TEMP
the temperature at which you are operating
=310
# PLUMED interprets the command:
# ff5: CONVERT_TO_FES GRID=histo5 TEMP=310
# as follows (Click the red comment above to revert to the short version of the input):
ff5The CUSTOM action with label ff5 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff5
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
=histo5 
FUNC
the function you wish to evaluate
=-2.57748*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)
=ff5 
FILE
 the file on which to write the grid
=mw_fes_adr_bin_tm3-tm6_1.dat

The DUMPGRID action with label  calculates somethingff6The CONVERT_TO_FES action with label ff6 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff6
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)
=histo6 
TEMP
the temperature at which you are operating
=310
# PLUMED interprets the command:
# ff6: CONVERT_TO_FES GRID=histo6 TEMP=310
# as follows (Click the red comment above to revert to the short version of the input):
ff6The CUSTOM action with label ff6 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff6
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
=histo6 
FUNC
the function you wish to evaluate
=-2.57748*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)
=ff6 
FILE
 the file on which to write the grid
=mw_fes_adr_bin_NPxxY.dat

ff7The CONVERT_TO_FES action with label ff7 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff7
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)
=histo7 
TEMP
the temperature at which you are operating
=310
# PLUMED interprets the command:
# ff7: CONVERT_TO_FES GRID=histo7 TEMP=310
# as follows (Click the red comment above to revert to the short version of the input):
ff7The CUSTOM action with label ff7 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff7
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
=histo7 
FUNC
the function you wish to evaluate
=-2.57748*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)
=ff7 
FILE
 the file on which to write the grid
=mw_fes_adr_bin_PIF_i.dat

ff9The CONVERT_TO_FES action with label ff9 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff9
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)
=histo9 
TEMP
the temperature at which you are operating
=310
# PLUMED interprets the command:
# ff9: CONVERT_TO_FES GRID=histo9 TEMP=310
# as follows (Click the red comment above to revert to the short version of the input):
ff9The CUSTOM action with label ff9 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff9
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
=histo9 
FUNC
the function you wish to evaluate
=-2.57748*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)
=ff9 
FILE
 the file on which to write the grid
=mw_fes_adr_bin_yy.dat

ff10The CONVERT_TO_FES action with label ff10 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff10
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)
=histo10 
TEMP
the temperature at which you are operating
=310
# PLUMED interprets the command:
# ff10: CONVERT_TO_FES GRID=histo10 TEMP=310
# as follows (Click the red comment above to revert to the short version of the input):
ff10The CUSTOM action with label ff10 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff10
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
=histo10 
FUNC
the function you wish to evaluate
=-2.57748*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)
=ff10 
FILE
 the file on which to write the grid
=mw_fes_adr_bin_tm5.dat

ff13The CONVERT_TO_FES action with label ff13 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff13
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)
=histo13 
TEMP
the temperature at which you are operating
=310
# PLUMED interprets the command:
# ff13: CONVERT_TO_FES GRID=histo13 TEMP=310
# as follows (Click the red comment above to revert to the short version of the input):
ff13The CUSTOM action with label ff13 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff13
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
=histo13 
FUNC
the function you wish to evaluate
=-2.57748*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)
=ff13 
FILE
 the file on which to write the grid
=mw_fes_adr_bin_tm3-tm6_2.dat