PLUMED-NEST

Project ID: plumID:19.071
Source: MFI_paper_scripts/reweighting/plumed_FB_rewe.dat
Originally used with PLUMED version: 2.4
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

p: 
READ
Read quantities from a colvar file. More details
  
FILE
the name of the file from which to read these quantities
=./position 
VALUES
the values to read from the file
=p.x 
IGNORE_FORCES
 use this flag if the forces added by any bias can be safely ignored
 
IGNORE_TIME
 ignore the time in the colvar file

The READ action with label p calculates the following quantities:
 Quantity   
 Description  
p..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for details
EXTERNAL
Calculate a restraint that is defined on a grid that is read during start up More details
 
ARG
the input for this action is the scalar output from one or more other actions
=p.x 
FILE
the name of the file containing the external potential
=grid.dat 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=metad

The EXTERNAL action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potentialbias: 
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
=120

The REWEIGHT_BIAS action with label bias calculates the following quantities:
 Quantity   
 Description  
bias.value
the weight to use for this frame to negate the effect the bias
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
 ...
  
ARG
the quantity that is being averaged
=p.x
  
GRID_MIN
 the lower bounds for the grid
=-2.6
  
GRID_MAX
 the upper bounds for the grid
=2.6
  
GRID_BIN
the number of bins for the grid
=500
  
BANDWIDTH
the bandwidths for kernel density esimtation
=0.04
  
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
=hh
... HISTOGRAM

The HISTOGRAM action with label hh calculates the following quantities:
 Quantity   
 Description  
hh.value
the estimate of the histogram as a function of the argument that was obtainedff: 
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
=120 


The CONVERT_TO_FES action with label ff calculates the following quantities:
 Quantity   
 Description  
ff.value
the free energy surface
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
=500