**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 quantity that is being averagedcv.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 esimtationLOGWEIGHTS=the logarithm of the quantity to use as the weights 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 to a free energy surface. More detailsGRID=the histogram that you would like to convert into a free energy surface (old syntax)hhTEMP=325the temperature at which you are operatingDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=the grid you would like to print (can also use ARG for specifying what is being printed)ffFILE=FES-reweight.datthe file on which to write the grid