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 file cvREADRead quantities from a colvar file. This action has hidden defaults. More detailsFILE=COLVAR-reweightthe name of the file from which to read these quantitiesVALUES=cont2the values to read from the fileIGNORE_TIME: wignore the time in the colvar fileREADRead quantities from a colvar file. This action has hidden defaults. 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. aa :ignore the time in the colvar fileREWEIGHT_BIASCalculate weights for ensemble averages that negate the effect the bias has on the region of phase space explored More detailsARG=wthe biases that must be taken into account when reweightingTEMP=325 # This command constructs the weighted histogram that appears inside the # logarithm in the equation above hhthe system temperatureHISTOGRAM...Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More detailsARG=cv.dist1the quantity that is being averagedGRID_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=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. ffthe logarithm of the quantity to use as the weights when calculating averagesCONVERT_TO_FESConvert a histogram to a free energy surface. This action is a shortcut. More detailsGRID=hhthe histogram that you would like to convert into a free energy surface (old syntax)TEMP=325 :the temperature at which you are operatingDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=ffthe grid you would like to print (can also use ARG for specifying what is being printed)FILE=FES-reweight.datthe file on which to write the grid