**Project ID:** plumID:20.018

**Source:** dimer/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 detailsNATURALuse natural unitsLOADLoads a library, possibly defining new actions. More detailsFILE=../src/bias/ReweightGeomFES.cppfile to be loadedDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=1,2the 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 actionsdistCOORDINATIONCalculate coordination numbers. More detailsGROUPA=1First list of atomsGROUPB=2Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.0The r_0 parameter of the switching functionD_0=0.75The d_0 parameter of the switching functionNN=1The n parameter of the switching functionLABEL=a label for the action so that its output can be referenced in the input to other actionscoordUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the input for this action is the scalar output from one or more other actionsdistAT=7.0the 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 actionswallsMETAD...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 actionscoordSIGMA=0.01the widths of the Gaussian hillsHEIGHT=0.25the heights of the Gaussian hillsPACE=2500the frequency for hill additionBIASFACTOR=10use well tempered metadynamics and use this bias factorTEMP=1.5the system temperature - this is only needed if you are doing well-tempered metadynamicsGRID_MIN=0.0the lower bounds for the gridGRID_MAX=1.0the upper bounds for the gridGRID_BIN=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=1.5the system temperatureLABEL=a label for the action so that its output can be referenced in the input to other actionsbiasREWEIGHT_GEOMFESTEMP=1.5 ARG=This action is not part of PLUMED and was included by using a LOAD command More detailscoordLABEL=geomHISTOGRAM...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 actionsdistGRID_MIN=0.0the lower bounds for the gridGRID_MAX=10.0the upper bounds for the gridGRID_BIN=1000the number of bins for the gridBANDWIDTH=0.05the bandwidths for kernel density estimationLOGWEIGHTS=list of actions that calculates log weights that should be used to weight configurations when calculating averagesbiasLABEL=a label for the action so that its output can be referenced in the input to other actionshdist... HISTOGRAMHISTOGRAM...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 actionscoordGRID_MIN=0.0the lower bounds for the gridGRID_MAX=1.0the upper bounds for the gridGRID_BIN=200the 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 averagesbiasLABEL=a label for the action so that its output can be referenced in the input to other actionshcoord... HISTOGRAMHISTOGRAM...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 actionscoordGRID_MIN=0.0the lower bounds for the gridGRID_MAX=1.0the upper bounds for the gridGRID_BIN=200the 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 averagesbias,geomLABEL=a label for the action so that its output can be referenced in the input to other actionshcoordg... HISTOGRAMCONVERT_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 usehdistTEMP=1.5the temperature at which you are operatingLABEL=a label for the action so that its output can be referenced in the input to other actionsfdistCONVERT_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 usehcoordTEMP=1.5the temperature at which you are operatingLABEL=a label for the action so that its output can be referenced in the input to other actionsfcoordCONVERT_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 usehcoordgTEMP=1.5the temperature at which you are operatingLABEL=a label for the action so that its output can be referenced in the input to other actionsfcoordgDUMPGRIDOutput 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 outputfdistFILE=fesdistthe file on which to write the gridSTRIDE=500000the 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 action that creates the grid you would like to outputfcoordFILE=fescoordthe file on which to write the gridSTRIDE=500000the 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 action that creates the grid you would like to outputfcoordgFILE=fescoordgthe file on which to write the gridSTRIDE=500000the 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=10000the 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 actionsdist,coord,b1.bias,b1.rctSTRIDE=1000the frequency with which the quantities of interest should be outputFILE=colvarthe name of the file on which to output these quantities