Project ID: plumID:19.080
Source: ohco2/symm-fes/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 energyDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=2,3the 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 actionsDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=1,2the pair of atom that we are calculating the distance betweenLABEL=d2a label for the action so that its output can be referenced in the input to other actionsCOORDINATIONCalculate coordination numbers. More detailsGROUPA=2First list of atomsGROUPB=3Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.75The r_0 parameter of the switching functionNN=4The n parameter of the switching functionLABEL=coorda label for the action so that its output can be referenced in the input to other actionsANGLECalculate an angle. More detailsATOMS=4,3,5the list of atoms involved in this collective variable (either 3 or 4 atoms)LABEL=anga label for the action so that its output can be referenced in the input to other actionsCOORDINATIONCalculate coordination numbers. More detailsGROUPA=3First list of atomsGROUPB=4Second 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=dis1a label for the action so that its output can be referenced in the input to other actionsCOORDINATIONCalculate coordination numbers. More detailsGROUPA=3First list of atomsGROUPB=5Second 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=dis2a 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=dis1,dis2the 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 actionsUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=d1the arguments on which the bias is actingAT=2.5the positions of the wallKAPPA=100.0the force constant for the wallLABEL=constrain1a 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=d2the arguments on which the bias is actingAT=1.3the positions of the wallKAPPA=500.0the force constant for the wallLABEL=constrain2a label for the action so that its output can be referenced in the input to other actionsEXTERNALCalculate a restraint that is defined on a grid that is read during start up More detailsARG=nmthe input for this action is the scalar output from one or more other actionsFILE=extbiasthe name of the file containing the external potentialLABEL=externala 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=1The minimum of the interval on which the basis functions are definedMAXIMUM=3.0The maximum of the interval on which the basis functions are definedORDER=48The order of the basis function expansion
td:TD_WELLTEMPEREDWell-tempered target distribution (dynamic). More detailsBIASFACTOR=30The bias factor used for the well-tempered distribution
# ExpansionVES_LINEAR_EXPANSION...Linear basis set expansion bias. More detailsARG=d1the 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=400the number of bins used for the gridTARGET_DISTRIBUTION=tdthe label of the target distribution to be usedLABEL=b1 ... 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=b1the label of the VES bias to be optimizedSTRIDE=4000the 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=0.5the step size used for the optimizationFES_OUTPUT=10how often the FES(s) should be written out to fileBIAS_OUTPUT=1000how often the bias(es) should be written out to fileFES_PROJ_OUTPUT=10how often the projections of the FES(s) should be written out to fileCOEFFS_OUTPUT=1how often the coefficients should be written to fileTARGETDIST_STRIDE=5 ... OPT_AVERAGED_SGDstride for updating a target distribution that is iteratively updated during the optimizationFLUSHThis 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=d1,d2,coord,ang,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