Project ID: plumID:20.010
Source: BiasedSimulations/16molecules/290K/plumed.start.dat
Originally used with PLUMED version: 2.6-dev
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
# vim:ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details.
vol:VOLUMECalculate the volume of the simulation box. More detailsENVIRONMENTSIMILARITY...Measure how similar the environment around atoms is to that found in some reference crystal structure. More detailsSPECIES=1-48:3this keyword is used for colvars such as coordination numberSIGMA=0.076the width to use for the gaussian kernelsCRYSTAL_STRUCTURE=CUSTOMTargeted crystal structureLABEL=refcva label for the action so that its output can be referenced in the input to other actionsREFERENCE_1=../../../Environments/IceIhExtendedEnvironments/env1.pdbPDB files with relative distances from central atomREFERENCE_2=../../../Environments/IceIhExtendedEnvironments/env2.pdbPDB files with relative distances from central atomREFERENCE_3=../../../Environments/IceIhExtendedEnvironments/env3.pdbPDB files with relative distances from central atomREFERENCE_4=../../../Environments/IceIhExtendedEnvironments/env4.pdbPDB files with relative distances from central atomMORE_THAN={RATIONAL R_0=0.5 NN=15 MM=30}calculate the number of variables that are more than a certain target valueMEAN... ENVIRONMENTSIMILARITYcalculate the mean of all the quantities
# Construct a bias potential using VES # # Basis functions
bf1:BF_LEGENDRELegendre polynomials basis functions. More detailsORDER=20The order of the basis function expansionMINIMUM=0.0The minimum of the interval on which the basis functions are definedMAXIMUM=16.0The maximum of the interval on which the basis functions are defined
# Target distribution
td_welltemp: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=refcv.morethanthe 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=290.0the system temperature - this is needed if the MD code does not pass the temperature to PLUMEDGRID_BINS=300the number of bins used for the gridTARGET_DISTRIBUTION=td_welltempthe 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=500the 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=2the step size used for the optimizationFES_OUTPUT=500how often the FES(s) should be written out to fileBIAS_OUTPUT=500how often the bias(es) should be written out to fileTARGETDIST_OUTPUT=500how often the dynamic target distribution(s) should be written out to fileCOEFFS_OUTPUT=100how often the coefficients should be written to fileTARGETDIST_STRIDE=500 #MULTIPLE_WALKERS ... OPT_AVERAGED_SGDstride for updating a target distribution that is iteratively updated during the optimizationQ6Calculate sixth order Steinhardt parameters. More detailsSPECIES=1-48:3this keyword is used for colvars such as coordination numberSWITCH={CUBIC D_0=0.3 D_MAX=0.35}the switching function that it used in the construction of the contact matrixVMEANcalculate the norm of the mean vectorLABEL=q6 diff:a label for the action so that its output can be referenced in the input to other actionsMATHEVALAn alias to the ef CUSTOM function. More detailsARG=q6.vmean,refcv.meanthe input to this functionFUNC=((x-0.15)/(0.4-0.15)-(y-0.4)/(0.6-0.4the function you wish to evaluatePERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=diffthe arguments on which the bias is actingAT=0.4the positions of the wallKAPPA=50000the force constant for the wallEXP=2the powers for the wallsLABEL=uwalla label for the action so that its output can be referenced in the input to other actionsPrint quantities to a file. More detailsSTRIDE=500the frequency with which the quantities of interest should be outputARGthe input for this action is the scalar output from one or more other actionsFILE=COLVARthe name of the file on which to output these quantities