Project ID: plumID:21.013
Source: h2-diss/ni001/plumed.inp
Originally used with PLUMED version: 2.6
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=../../data/ReweightGeomFES.cppfile to be loadedDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=65,66the pair of atom that we are calculating the distance betweenLABEL=d1a label for the action so that its output can be referenced in the input to other actionsDISTANCESCalculate the distances between multiple piars of atoms More detailsGROUPA=65-66Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBGROUPB=1-64Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBLESS_THAN={RATIONAL R_0=2.0}calculate the number of variables that are less than a certain target valueMIN={BETA=100.0}calculate the minimum valueLABEL=metalha 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=d1,metalh.minthe arguments on which the bias is actingAT=1.50,4.00the positions of the wallKAPPA=500,100the force constant for the wallLABEL=walla 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=d1,metalh.lessthanthe input to this functionCOEFFICIENTS=0.990,0.141the coefficients of the arguments in your functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionLABEL=cva 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=cvthe input for this action is the scalar output from one or more other actionsSIGMA=0.05the widths of the Gaussian hillsHEIGHT=0.25the heights of the Gaussian hillsPACE=1000the frequency for hill additionBIASFACTOR=25use well tempered metadynamics and use this bias factorTEMP=500the system temperature - this is only needed if you are doing well-tempered metadynamicsGRID_MIN=0.0the lower bounds for the gridGRID_MAX=4.0the upper bounds for the gridGRID_BIN=800the 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=500the system temperatureLABEL=biasa label for the action so that its output can be referenced in the input to other actionsREWEIGHT_GEOMFESTEMP=500 ARG=cv LABEL=gcvThis action is not part of PLUMED and was included by using a LOAD command More detailsREWEIGHT_GEOMFESTEMP=500 ARG=d1 LABEL=g1This action is not part of PLUMED and was included by using a LOAD command More detailsREWEIGHT_GEOMFESTEMP=500 ARG=metalh.lessthan LABEL=g2This action is not part of PLUMED and was included by using a LOAD command More detailsREWEIGHT_BIASCalculate weights for ensemble averages that negate the effect the bias has on the region of phase space explored More detailsTEMP=500the system temperatureARG=wall.biasthe biases that must be taken into account when reweightingLABEL=wbiasa 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=cvthe quantity that is being averagedGRID_MIN=0.0the lower bounds for the gridGRID_MAX=4.0the upper bounds for the gridGRID_BIN=3000the number of bins for the gridBANDWIDTH=0.01the bandwidths for kernel density esimtationLOGWEIGHTS=bias,wbiasthe logarithm of the quantity to use as the weights when calculating averagesCLEAR=5000000the frequency with whihc to clear the data that is being averagedLABEL=hh ... 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=cvthe quantity that is being averagedGRID_MIN=0.0the lower bounds for the gridGRID_MAX=4.0the upper bounds for the gridGRID_BIN=3000the number of bins for the gridBANDWIDTH=0.01the bandwidths for kernel density esimtationLOGWEIGHTS=bias,wbias,gcvthe logarithm of the quantity to use as the weights when calculating averagesCLEAR=5000000the frequency with whihc to clear the data that is being averagedLABEL=hhg ... 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=d1the quantity that is being averagedGRID_MIN=0.0the lower bounds for the gridGRID_MAX=2.0the upper bounds for the gridGRID_BIN=2000the number of bins for the gridBANDWIDTH=0.01the bandwidths for kernel density esimtationLOGWEIGHTS=bias,wbias,g1the logarithm of the quantity to use as the weights when calculating averagesCLEAR=5000000the frequency with whihc to clear the data that is being averagedLABEL=hh1 ... 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=metalh.lessthanthe quantity that is being averagedGRID_MIN=0.0the lower bounds for the gridGRID_MAX=6.0the upper bounds for the gridGRID_BIN=3000the number of bins for the gridBANDWIDTH=0.02the bandwidths for kernel density esimtationLOGWEIGHTS=bias,wbias,g2the logarithm of the quantity to use as the weights when calculating averagesCLEAR=5000000the frequency with whihc to clear the data that is being averagedLABEL=hh2 ... HISTOGRAMa label for the action so that its output can be referenced in the input to other actionsCONVERT_TO_FESConvert a histogram to a free energy surface. More detailsGRID=hhthe histogram that you would like to convert into a free energy surface (old syntax)TEMP=500.0the temperature at which you are operatingLABEL=ffa label for the action so that its output can be referenced in the input to other actionsCONVERT_TO_FESConvert a histogram to a free energy surface. More detailsGRID=hhgthe histogram that you would like to convert into a free energy surface (old syntax)TEMP=500.0the temperature at which you are operatingLABEL=ffga label for the action so that its output can be referenced in the input to other actionsCONVERT_TO_FESConvert a histogram to a free energy surface. More detailsGRID=hh1the histogram that you would like to convert into a free energy surface (old syntax)TEMP=500.0the temperature at which you are operatingLABEL=ff1a label for the action so that its output can be referenced in the input to other actionsCONVERT_TO_FESConvert a histogram to a free energy surface. More detailsGRID=hh2the histogram that you would like to convert into a free energy surface (old syntax)TEMP=500.0the temperature at which you are operatingLABEL=ff2a 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=ffthe grid you would like to print (can also use ARG for specifying what is being printed)FILE=festhe file on which to write the gridSTRIDE=1000000the 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=ffgthe grid you would like to print (can also use ARG for specifying what is being printed)FILE=fesgthe file on which to write the gridSTRIDE=1000000the 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=ff1the grid you would like to print (can also use ARG for specifying what is being printed)FILE=fes1the file on which to write the gridSTRIDE=1000000the 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=ff2the grid you would like to print (can also use ARG for specifying what is being printed)FILE=fes2the file on which to write the gridSTRIDE=1000000the 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=100000the frequency with which all the open files should be flushedPrint quantities to a file. More detailsARG=d1,metalh.lessthan,cv,b1.bias,b1.rctthe input for this action is the scalar output from one or more other actionsSTRIDE=10000the frequency with which the quantities of interest should be outputFILE=colvarthe name of the file on which to output these quantities