**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

# These first two commands instruct plumed to read in the quantities for each # trajectory frame that were computed using the previous input filecv:READRead quantities from a colvar file. More detailsFILE=COLVAR-reweightthe name of the file from which to read these quantitiesVALUES=cont2the values to read from the fileIGNORE_TIMEignore the time in the colvar filew:READRead quantities from a colvar file. More detailsFILE=COLVAR-reweightthe name of the file from which to read these quantitiesVALUES=biasthe values to read from the fileIGNORE_TIME# 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.ignore the time in the colvar fileaa:REWEIGHT_BIASCalculate weights for ensemble averages that negate the effect the bias has on the region of phase space explored More detailsARG=the biases that must be taken into account when reweightingwTEMP=325 # This command constructs the weighted histogram that appears inside the # logarithm in the equation abovethe system temperaturehh:HISTOGRAM...Accumulate the average probability density along a few CVs from a trajectory. More detailsARG=the input for this action is the scalar output from one or more other actionscv.dist1GRID_MIN=0the lower bounds for the gridGRID_MAX=6.5the upper bounds for the gridGRID_BIN=650the number of bins for the gridBANDWIDTH=0.02the bandwidths for kernel density estimationLOGWEIGHTS=list of actions that calculates log weights that should be used to weight configurations when calculating averagesaa... # 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_FESConvert a histogram, H(x), to a free energy surface using F(x) = -k_B T ln H(x). More detailsGRID=the action that creates the input grid you would like to usehhTEMP=325the temperature at which you are operatingDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=the action that creates the grid you would like to outputffFILE=FES-reweight.datthe file on which to write the grid