Project ID: plumID:19.081
Source: Na/02_References/Example/plumed.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.RESTARTActivate restart. More detailsLOADLoads a library, possibly defining new actions. More detailsFILE=../../../RefCV.cppfile to be loaded
energy:ENERGYCalculate the total potential energy of the simulation box. More details
vol:VOLUMECalculate the volume of the simulation box. More detailsREFCV... SPECIES=1-250 SIGMA=0.065 LATTICE_CONSTANTS=0.432 CRYSTAL_STRUCTURE=BCC LABEL=refcv MORE_THAN={RATIONAL R_0=0.5 NN=12 MM=24} MEAN ... REFCVThis action is not part of PLUMED and was included by using a LOAD command More details
# Construct a bias potential using VES # # Basis functions
bf1:BF_LEGENDRELegendre polynomials basis functions. More detailsORDER=10The order of the basis function expansionMINIMUM=0.0The minimum of the interval on which the basis functions are definedMAXIMUM=250.0The maximum of the interval on which the basis functions are defined
# Target distribution
td_welltemp:TD_WELLTEMPEREDWell-tempered target distribution (dynamic). More detailsBIASFACTOR=50The 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=350.0the 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_DUMMY...Dummy optimizer for debugging. 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 actionsCOEFFS_OUTPUT=10 ... OPT_DUMMYhow often the coefficients should be written to fileQ6Calculate sixth order Steinhardt parameters. More detailsSPECIES=1-250this keyword is used for colvars such as coordination numberSWITCH={CUBIC D_0=0.4 D_MAX=0.5}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-0.06540)/(0.4035-0.06540)-(y-0.33023)/(0.745086-0.33023the 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=0.1the positions of the wallKAPPA=100000the 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 detailsARGthe input for this action is the scalar output from one or more other actionsFILE=COLVARthe name of the file on which to output these quantitiesSTRIDE=500the frequency with which the quantities of interest should be output