**Project ID:** plumID:21.013

**Source:** h2-diss/ni211/plumed.inp

**Originally used with PLUMED version:** 2.6

**Stable:** zipped raw stdout - zipped raw stderr - stderr

**Master:** zipped raw stdout - zipped raw stderr - stderr

UNITSThis command sets the internal units for the code. More detailsLENGTH=Athe units of lengthsTIME=fsthe units of timeENERGY=kcal/molthe units of energyLOADLoads a library, possibly defining new actions. More detailsFILE=file to be loaded../../data/ReweightGeomFES.cppDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=109,110the pair of atom that we are calculating the distance betweenLABEL=a label for the action so that its output can be referenced in the input to other actionsd1DISTANCESCalculate the distances between multiple piars of atoms More detailsGROUPA=109-110Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBGROUPB=1-108Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBLESS_THAN={RATIONAL R_0=2.0}calculate the number of variables that are less than a certain target valueMIN={BETA=100.0}calculate the minimum valueLABEL=a label for the action so that its output can be referenced in the input to other actionsmetalhUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingd1,metalh.minAT=1.50,4.00the positions of the wallKAPPA=500,100the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionswallCOMBINECalculate a polynomial combination of a set of other variables. More detailsARG=the input to this functiond1,metalh.lessthanCOEFFICIENTS=0.993,0.118the coefficients of the arguments in your functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionLABEL=a label for the action so that its output can be referenced in the input to other actionscvMETAD...Used to performed metadynamics on one or more collective variables. More detailsARG=the input for this action is the scalar output from one or more other actionscvSIGMA=0.05the widths of the Gaussian hillsHEIGHT=0.25the heights of the Gaussian hillsPACE=1000the frequency for hill additionBIASFACTOR=25use well tempered metadynamics and use this bias factorTEMP=500the system temperature - this is only needed if you are doing well-tempered metadynamicsGRID_MIN=0.0the lower bounds for the gridGRID_MAX=3.0the upper bounds for the gridGRID_BIN=600the number of bins for the gridCALC_RCTcalculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]RCT_USTRIDE=1the update stride for calculating the c(t) reweighting factorLABEL=a label for the action so that its output can be referenced in the input to other actionsb1... METADREWEIGHT_METADCalculate the weights configurations should contribute to the histogram in a simulation in which a metadynamics bias acts upon the system. More detailsTEMP=500the system temperatureLABEL=a label for the action so that its output can be referenced in the input to other actionsbiasREWEIGHT_GEOMFESTEMP=500 ARG=This action is not part of PLUMED and was included by using a LOAD command More detailscvLABEL=gcvREWEIGHT_GEOMFESTEMP=500 ARG=This action is not part of PLUMED and was included by using a LOAD command More detailsd1LABEL=g1REWEIGHT_GEOMFESTEMP=500 ARG=This action is not part of PLUMED and was included by using a LOAD command More detailsmetalh.lessthanLABEL=g2REWEIGHT_BIASCalculate weights for ensemble averages that negate the effect the bias has on the region of phase space explored More detailsTEMP=500the system temperatureARG=the biases that must be taken into account when reweightingwall.biasLABEL=a label for the action so that its output can be referenced in the input to other actionswbiasHISTOGRAM...Accumulate the average probability density along a few CVs from a trajectory. More detailsARG=the quantity that is being averagedcvGRID_MIN=0.0the lower bounds for the gridGRID_MAX=3.0the upper bounds for the gridGRID_BIN=3000the number of bins for the gridBANDWIDTH=0.01the bandwidths for kernel density esimtationLOGWEIGHTS=the logarithm of the quantity to use as the weights when calculating averagesbias,wbiasCLEAR=5000000the frequency with whihc to clear the data that is being averagedLABEL=a label for the action so that its output can be referenced in the input to other actionshh... HISTOGRAMHISTOGRAM...Accumulate the average probability density along a few CVs from a trajectory. More detailsARG=the quantity that is being averagedcvGRID_MIN=0.0the lower bounds for the gridGRID_MAX=3.0the upper bounds for the gridGRID_BIN=3000the number of bins for the gridBANDWIDTH=0.01the bandwidths for kernel density esimtationLOGWEIGHTS=the logarithm of the quantity to use as the weights when calculating averagesbias,wbias,gcvCLEAR=5000000the frequency with whihc to clear the data that is being averagedLABEL=a label for the action so that its output can be referenced in the input to other actionshhg... HISTOGRAMHISTOGRAM...Accumulate the average probability density along a few CVs from a trajectory. More detailsARG=the quantity that is being averagedd1GRID_MIN=0.0the lower bounds for the gridGRID_MAX=2.0the upper bounds for the gridGRID_BIN=2000the number of bins for the gridBANDWIDTH=0.01the bandwidths for kernel density esimtationLOGWEIGHTS=the logarithm of the quantity to use as the weights when calculating averagesbias,wbias,g1CLEAR=5000000the frequency with whihc to clear the data that is being averagedLABEL=a label for the action so that its output can be referenced in the input to other actionshh1... HISTOGRAMHISTOGRAM...Accumulate the average probability density along a few CVs from a trajectory. More detailsARG=the quantity that is being averagedmetalh.lessthanGRID_MIN=0.0the lower bounds for the gridGRID_MAX=6.0the upper bounds for the gridGRID_BIN=3000the 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 averagesbias,wbias,g2CLEAR=5000000the frequency with whihc to clear the data that is being averagedLABEL=a label for the action so that its output can be referenced in the input to other actionshh2... HISTOGRAMCONVERT_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=500.0the temperature at which you are operatingLABEL=a label for the action so that its output can be referenced in the input to other actionsffCONVERT_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)hhgTEMP=500.0the temperature at which you are operatingLABEL=a label for the action so that its output can be referenced in the input to other actionsffgCONVERT_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)hh1TEMP=500.0the temperature at which you are operatingLABEL=a label for the action so that its output can be referenced in the input to other actionsff1CONVERT_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)hh2TEMP=500.0the temperature at which you are operatingLABEL=a label for the action so that its output can be referenced in the input to other actionsff2DUMPGRIDOutput 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=festhe file on which to write the gridSTRIDE=1000000the frequency with which the grid should be output to the fileDUMPGRIDOutput 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)ffgFILE=fesgthe file on which to write the gridSTRIDE=1000000the frequency with which the grid should be output to the fileDUMPGRIDOutput 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)ff1FILE=fes1the file on which to write the gridSTRIDE=1000000the frequency with which the grid should be output to the fileDUMPGRIDOutput 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)ff2FILE=fes2the file on which to write the gridSTRIDE=1000000the frequency with which the grid should be output to the fileFLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More detailsSTRIDE=100000the frequency with which all the open files should be flushedPrint quantities to a file. More detailsARG=the input for this action is the scalar output from one or more other actionsd1,metalh.lessthan,cv,b1.bias,b1.rctSTRIDE=10000the frequency with which the quantities of interest should be outputFILE=colvarthe name of the file on which to output these quantities