**Project ID:** plumID:20.018

**Source:** na/plumed.inp

**Originally used with PLUMED version:** 2.6-mod

**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=96.485the units of energyLOADLoads a library, possibly defining new actions. More detailsFILE=file to be loaded../src/bias/ReweightGeomFES.cppLOADLoads a library, possibly defining new actions. More detailsFILE=PairEntropy.cppfile to be loadedENERGYCalculate the total potential energy of the simulation box. More detailsLABEL=a label for the action so that its output can be referenced in the input to other actionseneVOLUMECalculate the volume of the simulation box. More detailsLABEL=a label for the action so that its output can be referenced in the input to other actionsvolCOMBINECalculate a polynomial combination of a set of other variables. More detailsARG=the input to this functionene,volCOEFFICIENTS=1.0,1.0/1602176.5the 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 actionsenthalpyCOMBINECalculate a polynomial combination of a set of other variables. More detailsARG=the input to this functionenthalpyCOEFFICIENTS=1.0/250the 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 actionsshCOORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More detailsSPECIES=1-250this keyword is used for colvars such as coordination numberSWITCH={RATIONAL D_0=5.0 R_0=0.1 D_MAX=6.0}the switching function that it used in the construction of the contact matrixMOMENTS=2the list of moments that you would like to calculateLABEL=a label for the action so that its output can be referenced in the input to other actionscnQ6Calculate sixth order Steinhardt parameters. More detailsSPECIES=1-250this keyword is used for colvars such as coordination numberSWITCH={RATIONAL D_0=5.0 R_0=0.1 D_MAX=6.0}the switching function that it used in the construction of the contact matrixMEANcalculate the mean of all the quantitiesLABEL=a label for the action so that its output can be referenced in the input to other actionsq6LOCAL_AVERAGECalculate averages over spherical regions centered on atoms More detailsSPECIES=this keyword is used for colvars such as coordination numberq6SWITCH={RATIONAL D_0=5.0 R_0=0.1 D_MAX=6.0}the switching function that it used in the construction of the contact matrixMEANcalculate the mean of all the quantitiesLABEL=a label for the action so that its output can be referenced in the input to other actionsq6lLOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingq6l.meanAT=0.0the positions of the wallKAPPA=1.0the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionsdummyPAIRENTROPY... ATOMS=1-250Calculate the KL Entropy from the radial distribution function More detailsMAXR=6.5 SIGMA=0.125 NHIST=130the maximum distance to use for the rdfLABEL=a label for the action so that its output can be referenced in the input to other actionsss... PAIRENTROPYMETAD...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 actionssh,ssSIGMA=0.002,0.10the widths of the Gaussian hillsHEIGHT=0.025the heights of the Gaussian hillsPACE=2500the frequency for hill additionBIASFACTOR=30use well tempered metadynamics and use this bias factorTEMP=375the system temperature - this is only needed if you are doing well-tempered metadynamicsGRID_MIN=-1.10,-6.0the lower bounds for the gridGRID_MAX=-0.95,-1.0the upper bounds for the gridGRID_BIN=750,500the 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=375the system temperatureLABEL=a label for the action so that its output can be referenced in the input to other actionsbiasREWEIGHT_GEOMFESARG=This action is not part of PLUMED and was included by using a LOAD command More detailsssTEMP=375 LABEL=gssREWEIGHT_GEOMFESARG=This action is not part of PLUMED and was included by using a LOAD command More detailsq6l.meanTEMP=375 LABEL=gq6lHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsARG=the quantity that is being averagedssGRID_MIN=-6.0the lower bounds for the gridGRID_MAX=-1.0the upper bounds for the gridGRID_BIN=1000the 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 averagesbiasLABEL=a label for the action so that its output can be referenced in the input to other actionshssHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsARG=the quantity that is being averagedq6l.meanGRID_MIN=0.05the lower bounds for the gridGRID_MAX=0.5the upper bounds for the gridGRID_BIN=900the number of bins for the gridBANDWIDTH=0.004the bandwidths for kernel density esimtationLOGWEIGHTS=the logarithm of the quantity to use as the weights when calculating averagesbiasLABEL=a label for the action so that its output can be referenced in the input to other actionshq6lHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsARG=the quantity that is being averagedssGRID_MIN=-6.0the lower bounds for the gridGRID_MAX=-1.0the upper bounds for the gridGRID_BIN=1000the 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,gssLABEL=a label for the action so that its output can be referenced in the input to other actionshssgHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsARG=the quantity that is being averagedq6l.meanGRID_MIN=0.05the lower bounds for the gridGRID_MAX=0.5the upper bounds for the gridGRID_BIN=900the number of bins for the gridBANDWIDTH=0.004the bandwidths for kernel density esimtationLOGWEIGHTS=the logarithm of the quantity to use as the weights when calculating averagesbias,gq6lLABEL=a label for the action so that its output can be referenced in the input to other actionshq6lgCONVERT_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)hssTEMP=375the temperature at which you are operatingLABEL=a label for the action so that its output can be referenced in the input to other actionsfssCONVERT_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)hq6lTEMP=375the temperature at which you are operatingLABEL=a label for the action so that its output can be referenced in the input to other actionsfq6lCONVERT_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)hssgTEMP=375the temperature at which you are operatingLABEL=a label for the action so that its output can be referenced in the input to other actionsfssgCONVERT_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)hq6lgTEMP=375the temperature at which you are operatingLABEL=a label for the action so that its output can be referenced in the input to other actionsfq6lgDUMPGRIDOutput 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)fssFILE=fesssthe file on which to write the gridSTRIDE=10000000the 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)fq6lFILE=fesq6lthe file on which to write the gridSTRIDE=10000000the 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)fssgFILE=fesssgthe file on which to write the gridSTRIDE=10000000the 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)fq6lgFILE=fesq6lgthe file on which to write the gridSTRIDE=10000000the 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=50000the 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 actionssh,ss,q6l.mean,b1.bias,b1.rctSTRIDE=50000the frequency with which the quantities of interest should be outputFILE=colvarthe name of the file on which to output these quantities