PLUMED-NEST

Project ID: plumID:19.071
Source: MFI_paper_scripts/reweighting/plumed_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 a scalar quantity
METAD
Used to performed metadynamics on one or more collective variables. More details
 ... 
ARG
the input for this action is the scalar output from one or more other actions
=p.x
SIGMA
the widths of the Gaussian hills
=0.05 
HEIGHT
the heights of the Gaussian hills
=0.1 
PACE
the frequency for hill addition
=500 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=5 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=metad 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=120
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 
REWEIGHTING_NGRID=200 
REWEIGHTING_NHILLS=10
... METAD


The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potentialbias: 
REWEIGHT_METAD
Calculate the weights configurations should contribute to the histogram in a simulation in which a metadynamics bias acts upon the system. More details
 
TEMP
the system temperature
=120

The REWEIGHT_METAD 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
=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

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
=120 


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