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
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 detailsLENGTH=Athe units of lengthsTIME=fsthe units of timeENERGY=96.485the units of energyLOADLoads a library, possibly defining new actions. More detailsFILE=../src/bias/ReweightGeomFES.cppfile to be loadedLOADLoads a library, possibly defining new actions. More detailsFILE=PairEntropy.cppfile to be loadedENERGYCalculate the total potential energy of the simulation box. More detailsLABEL=enea label for the action so that its output can be referenced in the input to other actionsVOLUMECalculate the volume of the simulation box. More detailsLABEL=vola label for the action so that its output can be referenced in the input to other actionsCOMBINECalculate a polynomial combination of a set of other variables. More detailsARG=ene,volthe input for this action is the scalar output from one or more other actionsCOEFFICIENTS=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=enthalpya label for the action so that its output can be referenced in the input to other actionsCOMBINECalculate a polynomial combination of a set of other variables. More detailsARG=enthalpythe input for this action is the scalar output from one or more other actionsCOEFFICIENTS=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=sha label for the action so that its output can be referenced in the input to other actionsCOORDINATIONNUMBERCalculate 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}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveMOMENTS=2calculate the moments of the distribution of collective variablesLABEL=cna label for the action so that its output can be referenced in the input to other actionsQ6Calculate 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}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveMEANtake the mean of these variablesLABEL=q6a label for the action so that its output can be referenced in the input to other actionsLOCAL_AVERAGECalculate averages over spherical regions centered on atoms More detailsSPECIES=q6this keyword is used for colvars such as coordination numberSWITCH={RATIONAL D_0=5.0 R_0=0.1 D_MAX=6.0}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveMEANtake the mean of these variablesLABEL=q6la label for the action so that its output can be referenced in the input to other actionsLOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=q6l.meanthe input for this action is the scalar output from one or more other actionsAT=0.0the positions of the wallKAPPA=1.0the force constant for the wallLABEL=dummya label for the action so that its output can be referenced in the input to other actionsPAIRENTROPY... ATOMS=1-250 MAXR=6.5 SIGMA=0.125 NHIST=130 LABEL=ss ... PAIRENTROPYThis action is not part of PLUMED and was included by using a LOAD command More detailsMETAD...Used to performed metadynamics on one or more collective variables. More detailsARG=sh,ssthe input for this action is the scalar output from one or more other actionsSIGMA=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=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=375the system temperatureLABEL=biasa label for the action so that its output can be referenced in the input to other actionsREWEIGHT_GEOMFESARG=ss TEMP=375 LABEL=gssThis action is not part of PLUMED and was included by using a LOAD command More detailsREWEIGHT_GEOMFESARG=q6l.mean TEMP=375 LABEL=gq6lThis action is not part of PLUMED and was included by using a LOAD command More detailsHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsARG=ssthe input for this action is the scalar output from one or more other actionsGRID_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 estimationLOGWEIGHTS=biaslist of actions that calculates log weights that should be used to weight configurations when calculating averagesLABEL=hssa label for the action so that its output can be referenced in the input to other actionsHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsARG=q6l.meanthe input for this action is the scalar output from one or more other actionsGRID_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 estimationLOGWEIGHTS=biaslist of actions that calculates log weights that should be used to weight configurations when calculating averagesLABEL=hq6la label for the action so that its output can be referenced in the input to other actionsHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsARG=ssthe input for this action is the scalar output from one or more other actionsGRID_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 estimationLOGWEIGHTS=bias,gsslist of actions that calculates log weights that should be used to weight configurations when calculating averagesLABEL=hssga label for the action so that its output can be referenced in the input to other actionsHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More detailsARG=q6l.meanthe input for this action is the scalar output from one or more other actionsGRID_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 estimationLOGWEIGHTS=bias,gq6llist of actions that calculates log weights that should be used to weight configurations when calculating averagesLABEL=hq6lga 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=hssthe action that creates the input grid you would like to useTEMP=375the temperature at which you are operatingLABEL=fssa 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=hq6lthe action that creates the input grid you would like to useTEMP=375the temperature at which you are operatingLABEL=fq6la 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=hssgthe action that creates the input grid you would like to useTEMP=375the temperature at which you are operatingLABEL=fssga 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=hq6lgthe action that creates the input grid you would like to useTEMP=375the temperature at which you are operatingLABEL=fq6lga 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=fssthe action that creates the grid you would like to outputFILE=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=fq6lthe action that creates the grid you would like to outputFILE=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=fssgthe action that creates the grid you would like to outputFILE=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=fq6lgthe action that creates the grid you would like to outputFILE=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=sh,ss,q6l.mean,b1.bias,b1.rctthe input for this action is the scalar output from one or more other actionsSTRIDE=50000the frequency with which the quantities of interest should be outputFILE=colvarthe name of the file on which to output these quantities