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
tested onv2.8
tested onmaster
# 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
w:
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. aa:
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 hh:
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
...
ARG
the input for this action is the scalar output from one or more other actions
=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 estimation
=0.02
LOGWEIGHTS
list of actions that calculates log weights that should be used to weight configurations 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. ff:
CONVERT_TO_FES
Convert a histogram, H(x), to a free energy surface using F(x) = -k_B T ln H(x). More details
GRID
the action that creates the input grid you would like to use
=hh
TEMP
the temperature at which you are operating
=325
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
GRID
the action that creates the grid you would like to output
=ff
FILE
the file on which to write the grid
=FES-reweight.dat