PLUMED-NEST

Project ID: plumID:23.044
Source: plumed_files/reweight_md.dat
Originally used with PLUMED version: 2.5
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

thetaThe READ action with label theta calculates the following quantities:
 Quantity   
 Type   
 Description  
theta
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
=../input_files/angles.dat 
VALUES
the values to read from the file
=theta 
IGNORE_TIME
 ignore the time in the colvar file
theta: 
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
=../input_files/angles.dat 
VALUES
the values to read from the file
=theta 
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
phiThe READ action with label phi calculates the following quantities:
 Quantity   
 Type   
 Description  
phi
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
=../input_files/angles.dat 
VALUES
the values to read from the file
=phi 
IGNORE_TIME
 ignore the time in the colvar file
phi: 
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
=../input_files/angles.dat 
VALUES
the values to read from the file
=phi 
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
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: 
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
=phi,theta 
GRID_MIN
 the lower bounds for the grid
=-pi,0 
GRID_MAX
 the upper bounds for the grid
=pi,pi 
GRID_BIN
the number of bins for the grid
=100,100 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.05,0.05 
KERNEL
 the kernel function you are using
=GAUSSIAN
hh: 
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
=phi,theta 
GRID_MIN
 the lower bounds for the grid
=-pi,0 
GRID_MAX
 the upper bounds for the grid
=pi,pi 
GRID_BIN
the number of bins for the grid
=100,100 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.05,0.05 
KERNEL
 the kernel function you are using
=GAUSSIAN  
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:
# hh: HISTOGRAM ARG=phi,theta GRID_MIN=-pi,0 GRID_MAX=pi,pi GRID_BIN=100,100 BANDWIDTH=0.05,0.05 KERNEL=GAUSSIAN
# 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
=phi,theta 
GRID_MIN
 the lower bounds for the grid
=-pi,0 
GRID_MAX
 the upper bounds for the grid
=pi,pi 
GRID_BIN
the number of bins for the grid
=100,100 
BANDWIDTH
the bandwidths for kernel density esimtation
=0.05,0.05 
KERNEL
 the kernel function you are using
=GAUSSIAN 
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
=0 
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
=0 
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
=298
# PLUMED interprets the command:
# ff: CONVERT_TO_FES GRID=hh TEMP=298
# 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
=-2.47771*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_2d.dat 
The DUMPGRID action with label  calculates something
ENDPLUMED
Terminate plumed input. More details