PLUMED-NEST

Project ID: plumID:19.050
Source: plumed_histogram.dat
Originally used with PLUMED version: not specified
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

# These first two commands instruct plumed to read in the quantities for each
# trajectory frame that were computed using the previous input file
cv: 
READ
Read quantities from a colvar file. More details
 
FILE
the name of the file from which to read these quantities
=COLVAR-reweight 
VALUES
the values to read from the file
=cont2 
IGNORE_TIME
 ignore the time in the colvar file
The READ action with label cv calculates the following quantities:
 Quantity   
 Description  
cv..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailsw: 
READ
Read quantities from a colvar file. More details
 
FILE
the name of the file from which to read these quantities
=COLVAR-reweight 
VALUES
the values to read from the file
=bias 
IGNORE_TIME
 ignore the time in the colvar file
# This command computes the reweighting factors for each of the frames in the
# trajectory from the simulation bias for that frame.  These reweighting factors
# are the exponential terms in the expression above.
The READ action with label w calculates the following quantities:
 Quantity   
 Description  
w..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailsaa: 
REWEIGHT_BIAS
Calculate weights for ensemble averages that negate the effect the bias has on the region of phase space explored More details
 
ARG
 the biases that must be taken into account when reweighting
=w 
TEMP
the system temperature
=325
# This command constructs the weighted histogram that appears inside the
# logarithm in the equation above
The REWEIGHT_BIAS action with label aa calculates the following quantities:
 Quantity   
 Description  
aa.value
the weight to use for this frame to negate the effect the biashh: 
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
 ...
  
ARG
the quantities that are being used to construct the histogram
=cv.dist1  
GRID_MIN
 the lower bounds for the grid
=0  
GRID_MAX
 the upper bounds for the grid
=6.5  
GRID_BIN
the number of bins for the grid
=650
  
BANDWIDTH
the bandwidths for kernel density esimtation
=0.02  
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=aa
...
# This first of these two commands takes the logarithm of the weighted
# histogram, while the second outputs the final free energy surface to a file.
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
=325
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-reweight.dat