**Project ID:** plumID:20.018

**Source:** da-tt/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=kcal/molthe units of energyLOADLoads 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 actionsd1DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=2,3the 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 actionsd2DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=3,4the 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 actionsd3DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=4,5the 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 actionsd4DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=5,6the 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 actionsd5DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=1,6the 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 actionsd6COMBINECalculate a polynomial combination of a set of other variables. More detailsARG=the input for this action is the scalar output from one or more other actionsd1,d2,d3,d4,d6COEFFICIENTS=-0.05,0.21,-0.08,0.69,0.69the 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 actionshldaUPPER_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 actionsd4,d6AT=5.0,5.0the positions of the wallKAPPA=50,50the 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 actionshldaSIGMA=0.15the widths of the Gaussian hillsHEIGHT=1.0the heights of the Gaussian hillsPACE=100the frequency for hill additionTTBIASFACTOR=25use transition tempered metadynamics with this bias factorCALC_TRANSITION_BIASSet to TRUE if you want to compute a metadynamics transition bias V*(t)TRANSITIONWELL0=2.0This keyword appears multiple times as TRANSITIONWELL followed by an integerTRANSITIONWELL1=5.0This keyword appears multiple times as TRANSITIONWELL followed by an integerTEMP=600the system temperature - this is only needed if you are doing well-tempered metadynamicsGRID_MIN=1.0the lower bounds for the gridGRID_MAX=9.0the upper bounds for the gridGRID_BIN=1600the 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_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 reweightingb1.biasTEMP=600the 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 detailshldaTEMP=600 LABEL=ghldaHISTOGRAMAccumulate 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 actionshldaGRID_MIN=1.0the lower bounds for the gridGRID_MAX=9.0the upper bounds for the gridGRID_BIN=4000the number of bins for the gridBANDWIDTH=0.01the 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 actionshhldaHISTOGRAMAccumulate 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 actionshldaGRID_MIN=1.0the lower bounds for the gridGRID_MAX=9.0the upper bounds for the gridGRID_BIN=4000the number of bins for the gridBANDWIDTH=0.01the bandwidths for kernel density estimationLOGWEIGHTS=list of actions that calculates log weights that should be used to weight configurations when calculating averagesbias,ghldaLABEL=a label for the action so that its output can be referenced in the input to other actionshhldagCONVERT_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 usehhldaTEMP=600the temperature at which you are operatingLABEL=a label for the action so that its output can be referenced in the input to other actionsfhldaCONVERT_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 usehhldagTEMP=600the temperature at which you are operatingLABEL=a label for the action so that its output can be referenced in the input to other actionsfhldagDUMPGRIDOutput 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 outputfhldaFILE=feshldathe 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 outputfhldagFILE=feshldagthe 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=2000the 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 actionsd4,d6,hlda,b1.bias,b1.rctSTRIDE=200the frequency with which the quantities of interest should be outputFILE=colvarthe name of the file on which to output these quantities