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. 

refcv: 
READ
Read quantities from a colvar file. 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
The READ action with label refcv calculates a scalar quantityb1: 
READ
Read quantities from a colvar file. 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
The READ action with label b1 calculates a scalar quantityuwall: 
READ
Read quantities from a colvar file. 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

The READ action with label uwall calculates a scalar quantitybias: 
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

The REWEIGHT_BIAS action with label bias calculates a scalar quantity
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. 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
... HISTOGRAM

ff: 
CONVERT_TO_FES
Convert a histogram to a free energy surface. 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

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

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