PLUMED-NEST

Project ID: plumID:19.081
Source: Na/02_References/Example/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. 

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
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

biasThe REWEIGHT_BIAS 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 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
=350.0 
ARG
 the biases that must be taken into account when reweighting
=b1.bias,uwall.bias

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
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hhThe HISTOGRAM action with label hh calculates the following quantities:
 Quantity   
 Type   
 Description  
hh
grid
the estimate of the histogram as a function of the argument that was obtained
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=bias
  
STRIDE
 the frequency with which to store data for averaging
=1
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=5000
... 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
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hh
  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=bias
  
STRIDE
 the frequency with which to store data for averaging
=1
  
CLEAR
 the frequency with whihc to clear the data that is being averaged
=5000
 
NORMALIZATION
 This controls how the data is normalized it can be set equal to true, false or ndata
=ndata
... HISTOGRAM
# PLUMED interprets the command:
# HISTOGRAM ...
#   ARG=refcv.morethan
#   GRID_MIN=-0.5
#   GRID_MAX=250.5
#   GRID_BIN=1000
#   BANDWIDTH=1.
#   LABEL=hh
#   LOGWEIGHTS=bias
#   STRIDE=1
#   CLEAR=5000
# ... HISTOGRAM
# as follows (Click the red comment above to revert to the short version of the input):
hh_weightThe CONSTANT action with label hh_weight calculates the following quantities:
 Quantity   
 Type   
 Description  
hh_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
hh_kdeThe KDE action with label hh_kde calculates the following quantities:
 Quantity   
 Type   
 Description  
hh_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 
hh_kdepThe CUSTOM action with label hh_kdep calculates the following quantities:
 Quantity   
 Type   
 Description  
hh_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
=hh_kde,hh_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 
hh_uThe ACCUMULATE action with label hh_u calculates the following quantities:
 Quantity   
 Type   
 Description  
hh_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
=hh_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
=5000 
hh_nsumThe ACCUMULATE action with label hh_nsum calculates the following quantities:
 Quantity   
 Type   
 Description  
hh_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
=hh_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
=5000 
hhThe CUSTOM action with label hh calculates the following quantities:
 Quantity   
 Type   
 Description  
hh
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
=hh_u,hh_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 --- 
ffThe CONVERT_TO_FES action with label ff calculates the following quantities:
 Quantity   
 Type   
 Description  
ff
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)
=hh 
TEMP
the temperature at which you are operating
=350.0
# PLUMED interprets the command:
# ff: CONVERT_TO_FES GRID=hh TEMP=350.0
# as follows (Click the red comment above to revert to the short version of the input):
ffThe CUSTOM action with label ff calculates the following quantities:
 Quantity   
 Type   
 Description  
ff
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
=hh 
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)
=ff 
FILE
 the file on which to write the grid
=fes 
STRIDE
 the frequency with which the grid should be output to the file
=5000

The DUMPGRID action with label  calculates something
PRINT
Print quantities to a file. More details
 
STRIDE
 the frequency with which the quantities of interest should be output
=1  
ARG
the input for this action is the scalar output from one or more other actions
 
FILE
the name of the file on which to output these quantities
=COLVAR