PLUMED-NEST

Project ID: plumID:23.016
Source: plumed_reweight_2D_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
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
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
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

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,yy
BANDWIDTH
the bandwidths for kernel density esimtation
=0.02,0.02
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
=histo1The HISTOGRAM action with label histo1 calculates the following quantities:
 Quantity   
 Type   
 Description  
histo1
grid
the estimate of the histogram as a function of the argument that was obtained
GRID_MIN
 the lower bounds for the grid
=0.53,0.29
GRID_MAX
 the upper bounds for the grid
=1.85,1.80
GRID_BIN
the number of bins for the grid
=150,150
...
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,yy
BANDWIDTH
the bandwidths for kernel density esimtation
=0.02,0.02
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
=histo1
GRID_MIN
 the lower bounds for the grid
=0.53,0.29
GRID_MAX
 the upper bounds for the grid
=1.85,1.80
GRID_BIN
the number of bins for the grid
=150,150
 
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,yy
# BANDWIDTH=0.02,0.02
# LOGWEIGHTS=bias
# LABEL=histo1
# GRID_MIN=0.53,0.29
# GRID_MAX=1.85,1.80
# GRID_BIN=150,150
# ...
# as follows (Click the red comment above to revert to the short version of the input):
histo1_weightThe CONSTANT action with label histo1_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
histo1_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
histo1_kdeThe KDE action with label histo1_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
histo1_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,yy 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.02,0.02 
GRID_MIN
 the lower bounds for the grid
=0.53,0.29 
GRID_MAX
 the upper bounds for the grid
=1.85,1.80 
GRID_BIN
the number of bins for the grid
=150,150 
histo1_kdepThe CUSTOM action with label histo1_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
histo1_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
=histo1_kde,histo1_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 
histo1_uThe ACCUMULATE action with label histo1_u calculates the following quantities:
 Quantity   
 Type   
 Description  
histo1_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
=histo1_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 
histo1_nsumThe ACCUMULATE action with label histo1_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
histo1_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
=histo1_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 
histo1The CUSTOM action with label histo1 calculates the following quantities:
 Quantity   
 Type   
 Description  
histo1
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
=histo1_u,histo1_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_1,NPxxY_i
BANDWIDTH
the bandwidths for kernel density esimtation
=0.02,0.02
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
=histo2The HISTOGRAM action with label histo2 calculates the following quantities:
 Quantity   
 Type   
 Description  
histo2
grid
the estimate of the histogram as a function of the argument that was obtained
GRID_MIN
 the lower bounds for the grid
=0.53,0.06
GRID_MAX
 the upper bounds for the grid
=1.85,0.72
GRID_BIN
the number of bins for the grid
=150,150
...
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,NPxxY_i
BANDWIDTH
the bandwidths for kernel density esimtation
=0.02,0.02
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
=histo2
GRID_MIN
 the lower bounds for the grid
=0.53,0.06
GRID_MAX
 the upper bounds for the grid
=1.85,0.72
GRID_BIN
the number of bins for the grid
=150,150
 
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,NPxxY_i
# BANDWIDTH=0.02,0.02
# LOGWEIGHTS=bias
# LABEL=histo2
# GRID_MIN=0.53,0.06
# GRID_MAX=1.85,0.72
# GRID_BIN=150,150
# ...
# as follows (Click the red comment above to revert to the short version of the input):
histo2_weightThe CONSTANT action with label histo2_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
histo2_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
histo2_kdeThe KDE action with label histo2_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
histo2_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,NPxxY_i 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.02,0.02 
GRID_MIN
 the lower bounds for the grid
=0.53,0.06 
GRID_MAX
 the upper bounds for the grid
=1.85,0.72 
GRID_BIN
the number of bins for the grid
=150,150 
histo2_kdepThe CUSTOM action with label histo2_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
histo2_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
=histo2_kde,histo2_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 
histo2_uThe ACCUMULATE action with label histo2_u calculates the following quantities:
 Quantity   
 Type   
 Description  
histo2_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
=histo2_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 
histo2_nsumThe ACCUMULATE action with label histo2_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
histo2_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
=histo2_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 
histo2The CUSTOM action with label histo2 calculates the following quantities:
 Quantity   
 Type   
 Description  
histo2
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
=histo2_u,histo2_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_1,PIF_i
BANDWIDTH
the bandwidths for kernel density esimtation
=0.02,0.02
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
=histo3The HISTOGRAM action with label histo3 calculates the following quantities:
 Quantity   
 Type   
 Description  
histo3
grid
the estimate of the histogram as a function of the argument that was obtained
GRID_MIN
 the lower bounds for the grid
=0.53,0.0
GRID_MAX
 the upper bounds for the grid
=1.85,0.74
GRID_BIN
the number of bins for the grid
=150,150
...
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,PIF_i
BANDWIDTH
the bandwidths for kernel density esimtation
=0.02,0.02
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
=histo3
GRID_MIN
 the lower bounds for the grid
=0.53,0.0
GRID_MAX
 the upper bounds for the grid
=1.85,0.74
GRID_BIN
the number of bins for the grid
=150,150
 
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,PIF_i
# BANDWIDTH=0.02,0.02
# LOGWEIGHTS=bias
# LABEL=histo3
# GRID_MIN=0.53,0.0
# GRID_MAX=1.85,0.74
# GRID_BIN=150,150
# ...
# as follows (Click the red comment above to revert to the short version of the input):
histo3_weightThe CONSTANT action with label histo3_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
histo3_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
histo3_kdeThe KDE action with label histo3_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
histo3_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,PIF_i 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.02,0.02 
GRID_MIN
 the lower bounds for the grid
=0.53,0.0 
GRID_MAX
 the upper bounds for the grid
=1.85,0.74 
GRID_BIN
the number of bins for the grid
=150,150 
histo3_kdepThe CUSTOM action with label histo3_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
histo3_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
=histo3_kde,histo3_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 
histo3_uThe ACCUMULATE action with label histo3_u calculates the following quantities:
 Quantity   
 Type   
 Description  
histo3_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
=histo3_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 
histo3_nsumThe ACCUMULATE action with label histo3_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
histo3_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
=histo3_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 
histo3The CUSTOM action with label histo3 calculates the following quantities:
 Quantity   
 Type   
 Description  
histo3
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
=histo3_u,histo3_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 --- 
ff1The CONVERT_TO_FES action with label ff1 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff1
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)
=histo1 
TEMP
the temperature at which you are operating
=310
# PLUMED interprets the command:
# ff1: CONVERT_TO_FES GRID=histo1 TEMP=310
# as follows (Click the red comment above to revert to the short version of the input):
ff1The CUSTOM action with label ff1 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff1
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
=histo1 
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)
=ff1 
FILE
 the file on which to write the grid
=mw_fes_adr_bin_tm3-tm6_yy.dat

The DUMPGRID action with label  calculates somethingff2The CONVERT_TO_FES action with label ff2 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff2
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)
=histo2 
TEMP
the temperature at which you are operating
=310
# PLUMED interprets the command:
# ff2: CONVERT_TO_FES GRID=histo2 TEMP=310
# as follows (Click the red comment above to revert to the short version of the input):
ff2The CUSTOM action with label ff2 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff2
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
=histo2 
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)
=ff2 
FILE
 the file on which to write the grid
=mw_fes_adr_bin_tm3-tm6_NPxxY.dat

ff3The CONVERT_TO_FES action with label ff3 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff3
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)
=histo3 
TEMP
the temperature at which you are operating
=310
# PLUMED interprets the command:
# ff3: CONVERT_TO_FES GRID=histo3 TEMP=310
# as follows (Click the red comment above to revert to the short version of the input):
ff3The CUSTOM action with label ff3 calculates the following quantities:
 Quantity   
 Type   
 Description  
ff3
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
=histo3 
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)
=ff3 
FILE
 the file on which to write the grid
=mw_fes_adr_bin_tm3-tm6_PIF.dat