Project ID: plumID:19.080
Source: ohco2/asymm-param/plumed.inp
Originally used with PLUMED version: 2.4.1
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 energyCOORDINATIONCalculate 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=1.15The r_0 parameter of the switching functionNN=12The n parameter of the switching functionLABEL=d1a 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=3Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.15The r_0 parameter of the switching functionNN=12The n parameter of the switching functionLABEL=d2a 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,d2the input to this functionCOEFFICIENTS=0.5,-0.5the coefficients of the arguments in your functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionLABEL=nma label for the action so that its output can be referenced in the input to other actions
bf1:BF_CHEBYSHEVChebyshev polynomial basis functions. More detailsMINIMUM=-0.5The minimum of the interval on which the basis functions are definedMAXIMUM=0.5The maximum of the interval on which the basis functions are definedORDER=48The order of the basis function expansion
td:TD_GRIDTarget distribution from an external grid file (static). More detailsFILE=histoThe name of the external grid file to be used as a target distribution
# ExpansionVES_LINEAR_EXPANSION...Linear basis set expansion bias. More detailsARG=nmthe input for this action is the scalar output from one or more other actionsBASIS_FUNCTIONS=bf1the label of the one dimensional basis functions that should 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 gridTARGET_DISTRIBUTION=tdthe label of the target distribution to be usedLABEL=external ... VES_LINEAR_EXPANSIONa label for the action so that its output can be referenced in the input to other actions
# Optimization algorithmOPT_AVERAGED_SGD...Averaged stochastic gradient decent with fixed step size. More detailsBIAS=externalthe label of the VES bias to be optimizedSTRIDE=2000the frequency of updating the coefficients given in the number of MD stepsLABEL=o1a label for the action so that its output can be referenced in the input to other actionsSTEPSIZE=0.25the step size used for the optimizationFES_OUTPUT=1000how often the FES(s) should be written out to fileBIAS_OUTPUT=10how often the bias(es) should be written out to fileFES_PROJ_OUTPUT=20how often the projections of the FES(s) should be written out to fileCOEFFS_OUTPUT=1 ... OPT_AVERAGED_SGDhow often the coefficients should be written to fileFLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More detailsSTRIDE=200the frequency with which all the open files should be flushedPrint quantities to a file. More detailsARG=nm,external.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