Project ID: plumID:21.020
Source: hbr/ves/plumed.inp
Originally used with PLUMED version: 2.8
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 time
d1:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=10,11the pair of atom that we are calculating the distance betweenNOPBCd2:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=11,1the pair of atom that we are calculating the distance betweenNOPBCd3:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=10,2the pair of atom that we are calculating the distance betweenNOPBCd4:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=11,2the pair of atom that we are calculating the distance betweenNOPBCd5:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=10,1the pair of atom that we are calculating the distance betweenNOPBCd6:ignore the periodic boundary conditions when calculating distancesDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=1,2the pair of atom that we are calculating the distance betweenNOPBCignore the periodic boundary conditions when calculating distances
uwall:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=d1,d2,d3,d4,d5,d6the arguments on which the bias is actingAT=3.0,3.0,3.0,3.0,3.0,3.0the positions of the wallKAPPA=100,100,100,100,100,100the force constant for the wall
cv:COMBINECalculate a polynomial combination of a set of other variables. More detailsARG=d1,d2,d3,d4,d5,d6the input to this functionCOEFFICIENTS=0.661,-0.656,-0.328,0.011,-0.021,0.157the coefficients of the arguments in your functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionBF_CHEBYSHEVChebyshev polynomial basis functions. More detailsMINIMUM=-3.0The minimum of the interval on which the basis functions are definedMAXIMUM=2.0The maximum of the interval on which the basis functions are definedORDER=48The order of the basis function expansionLABEL=bfa label for the action so that its output can be referenced in the input to other actionsTD_WELLTEMPEREDWell-tempered target distribution (dynamic). More detailsBIASFACTOR=50The bias factor used for the well-tempered distributionLABEL=tda label for the action so that its output can be referenced in the input to other actionsVES_LINEAR_EXPANSIONLinear basis set expansion bias. More detailsARG=cvthe input for this action is the scalar output from one or more other actionsBASIS_FUNCTIONS=bfthe label of the one dimensional basis functions that should be usedTARGET_DISTRIBUTION=tdthe label of the target distribution to be usedTEMP=300the system temperature - this is needed if the MD code does not pass the temperature to PLUMEDGRID_BINS=500the number of bins used for the gridLABEL=b1a label for the action so that its output can be referenced in the input to other actionsOPT_AVERAGED_SGDAveraged stochastic gradient decent with fixed step size. More detailsBIAS=b1the label of the VES bias to be optimizedSTRIDE=200the frequency of updating the coefficients given in the number of MD stepsSTEPSIZE=5.0the step size used for the optimizationTARGETDIST_STRIDE=10stride for updating a target distribution that is iteratively updated during the optimizationFES_OUTPUT=1000how often the FES(s) should be written out to fileLABEL=opta label for the action so that its output can be referenced in the input to other actionsREWEIGHT_BIASCalculate weights for ensemble averages that negate the effect the bias has on the region of phase space explored More detailsARG=b1.biasthe biases that must be taken into account when reweightingTEMP=300the system temperatureLABEL=biasa 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=-2.0the lower bounds for the gridGRID_MAX=2.0the upper bounds for the gridGRID_BIN=4000the number of bins for the gridBANDWIDTH=0.02the bandwidths for kernel density esimtationCLEAR=200000the frequency with whihc to clear the data that is being averagedLOGWEIGHTS=biasthe logarithm of the quantity to use as the weights when calculating averagesLABEL=hh ... 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=300.0the temperature at which you are operatingLABEL=ffa 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=200000the 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=d1,d2,d3,d4,d5,d6,cv,b1.biasthe input for this action is the scalar output from one or more other actionsSTRIDE=200the frequency with which the quantities of interest should be outputFILE=colvarthe name of the file on which to output these quantities