Project ID: plumID:20.010
Source: BiasedSimulations/288molecules/290K/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 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=1-864:3this keyword is used for colvars such as coordination numberSIGMA=0.055the 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=12 MM=24}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=288.0The maximum of the interval on which the basis functions are defined
# Target distribution
td_welltemp:TD_WELLTEMPEREDWell-tempered target distribution (dynamic). More detailsBIASFACTOR=100The 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_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=o1 #MULTIPLE_WALKERSa label for the action so that its output can be referenced in the input to other actionsCOEFFS_OUTPUT=100 ... OPT_DUMMYhow often the coefficients should be written to fileENVIRONMENTSIMILARITY...Measure how similar the environment around atoms is to that found in some reference crystal structure. More detailsSPECIES=1-864:3this keyword is used for colvars such as coordination numberSIGMA=0.055the width to use for the gaussian kernelsCRYSTAL_STRUCTURE=CUSTOMTargeted crystal structureLABEL=refcv2a label for the action so that its output can be referenced in the input to other actionsREFERENCE_1=../../../Environments/IceIcExtendedEnvironments/env1.pdbPDB files with relative distances from central atomREFERENCE_2=../../../Environments/IceIcExtendedEnvironments/env2.pdbPDB files with relative distances from central atomMORE_THAN={RATIONAL R_0=0.5 NN=12 MM=24}calculate the number of variables that are more than a certain target valueMEAN... ENVIRONMENTSIMILARITYcalculate the mean of all the quantities
diff:MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More detailsARG=refcv2.mean,refcv.meanthe input to this functionFUNC=((x-0.26)/(0.58-0.26)-(y-0.29)/(0.80-0.29the 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=0.04the 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 actions
# Avoid other structuresQ6Calculate sixth order Steinhardt parameters. More detailsSPECIES=1-288:3this 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 diff2:a label for the action so that its output can be referenced in the input to other actionsMATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More detailsARG=q6.vmean,refcv.meanthe input to this functionFUNC=((x-0.0668781995)/(0.39184059-0.0668781995)-(y-0.2899390548628429)/(0.7838534089775562-0.2899390548628429the function you wish to evaluatePERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionPrint 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