Project ID: plumID:21.002
Source: Crystallization/IceIh/288molecules/350K/plumed.dat
Originally used with PLUMED version: 2.8
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
#SETTINGS NREPLICAS=2# vim:ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details.
#RESTART
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=0.05the 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=env1h.pdbPDB files with relative distances from central atomREFERENCE_2=env2h.pdbPDB files with relative distances from central atomREFERENCE_3=env3h.pdbPDB files with relative distances from central atomREFERENCE_4=env4h.pdbPDB files with relative distances from central atomMORE_THAN={RATIONAL R_0=0.5 NN=6 MM=12}calculate the number of variables that are more than a certain target valueMEAN... ENVIRONMENTSIMILARITYcalculate the mean of all the quantities
# Construct a bias potential
energy:ENERGYCalculate the total potential energy of the simulation box. More details
# Construct a bias potential using VES # # Basis functions
bf1:BF_LEGENDRELegendre polynomials basis functions. More detailsORDER=40The 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_uni:TD_UNIFORMUniform target distribution (static). More details
# 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_unithe 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=0.5the 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 fileCOEFFS_OUTPUT=100 #MULTIPLE_WALKERS ... OPT_AVERAGED_SGDhow 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=0.05the 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=env1c.pdbPDB files with relative distances from central atomREFERENCE_2=env2c.pdbPDB files with relative distances from central atomMORE_THAN={RATIONAL R_0=0.5 NN=6 MM=12}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 ef CUSTOM function. More detailsARG=refcv2.mean,refcv.meanthe input to this functionFUNC=((x-0.2075)/(0.5821-0.2075)-(y-0.2319)/(0.8137-0.2319the 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=0.05the 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=1-864:3this 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 ef CUSTOM function. More detailsARG=q6.vmean,refcv.meanthe input to this functionFUNC=((x-0.0402)/(0.4404-0.0402)-(y-0.2319)/(0.8137-0.2319the 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=diff2the arguments on which the bias is actingAT=0.05the positions of the wallKAPPA=100000the force constant for the wallEXP=2the powers for the wallsLABEL=uwall2a 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