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
Click on the labels of the actions for more information on what each action computes
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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=dista label for the action so that its output can be referenced in the input to other actionsCOORDINATIONCalculate 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=coorda label for the action so that its output can be referenced in the input to other actionsUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=distthe input for this action is the scalar output from one or more other actionsAT=7.0the positions of the wallKAPPA=1.0the force constant for the wallLABEL=wallsa label for the action so that its output can be referenced in the input to other actionsMETAD...Used to performed metadynamics on one or more collective variables. More detailsARG=coordthe input for this action is the scalar output from one or more other actionsSIGMA=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=b1 ... METADa label for the action so that its output can be referenced in the input to other actionsREWEIGHT_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=biasa label for the action so that its output can be referenced in the input to other actionsREWEIGHT_GEOMFESTEMP=1.5 ARG=coord LABEL=geomThis action is not part of PLUMED and was included by using a LOAD command More detailsHISTOGRAM...Accumulate the average probability density along a few CVs from a trajectory. More detailsARG=distthe input for this action is the scalar output from one or more other actionsGRID_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=biaslist of actions that calculates log weights that should be used to weight configurations when calculating averagesLABEL=hdist ... HISTOGRAMa label for the action so that its output can be referenced in the input to other actionsHISTOGRAM...Accumulate the average probability density along a few CVs from a trajectory. More detailsARG=coordthe input for this action is the scalar output from one or more other actionsGRID_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=biaslist of actions that calculates log weights that should be used to weight configurations when calculating averagesLABEL=hcoord ... HISTOGRAMa label for the action so that its output can be referenced in the input to other actionsHISTOGRAM...Accumulate the average probability density along a few CVs from a trajectory. More detailsARG=coordthe input for this action is the scalar output from one or more other actionsGRID_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=bias,geomlist of actions that calculates log weights that should be used to weight configurations when calculating averagesLABEL=hcoordg ... HISTOGRAMa label for the action so that its output can be referenced in the input to other actionsCONVERT_TO_FESConvert a histogram, H(x), to a free energy surface using F(x) = -k_B T ln H(x). More detailsGRID=hdistthe action that creates the input grid you would like to useTEMP=1.5the temperature at which you are operatingLABEL=fdista label for the action so that its output can be referenced in the input to other actionsCONVERT_TO_FESConvert a histogram, H(x), to a free energy surface using F(x) = -k_B T ln H(x). More detailsGRID=hcoordthe action that creates the input grid you would like to useTEMP=1.5the temperature at which you are operatingLABEL=fcoorda label for the action so that its output can be referenced in the input to other actionsCONVERT_TO_FESConvert a histogram, H(x), to a free energy surface using F(x) = -k_B T ln H(x). More detailsGRID=hcoordgthe action that creates the input grid you would like to useTEMP=1.5the temperature at which you are operatingLABEL=fcoordga label for the action so that its output can be referenced in the input to other actionsDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=fdistthe action that creates the grid you would like to outputFILE=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=fcoordthe action that creates the grid you would like to outputFILE=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=fcoordgthe action that creates the grid you would like to outputFILE=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=dist,coord,b1.bias,b1.rctthe input for this action is the scalar output from one or more other actionsSTRIDE=1000the frequency with which the quantities of interest should be outputFILE=colvarthe name of the file on which to output these quantities