Project ID: plumID:23.002
Source: 1_Metadynamics/2_Entropy/plumed.dat
Originally used with PLUMED version: 2.5.1
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

Click on the labels of the actions for more information on what each action computes
tested onv2.10
tested onmaster
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UNITSThis command sets the internal units for the code. More details NATURAL use natural units

ene: ENERGYCalculate the total potential energy of the simulation box. More details e: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=ene FUNCthe function you wish to evaluate=x/4394.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO s: PAIRENTROPYCalculate the KL Entropy from the radial distribution function More details ATOMSthe atoms that are being used to calculate the RDF=1-4394 MAXRthe maximum distance to use for the rdf=2.5 SIGMA an alternative method for specifying the bandwidth instead of using the BANDWIDTH keyword=0.05 NLIST NL_CUTOFF=2.8 NL_STRIDE=10 PIVCalculates the PIV-distance. More details ... LABELa label for the action so that its output can be referenced in the input to other actions=c1 PRECISIONthe precision for approximating reals with integers in sorting=1000 VOLUMEScale atom-atom distances by the cubic root of the cell volume=1 NLIST Use a neighbor list for distance calculations REF_FILEPDB file name that contains the ith reference structure=Liq.pdb PIVATOMSNumber of atoms to use for PIV=2 ATOMTYPESThe atom types to use for PIV=1,2 SFACTORScale the PIV-distance by such block-specific factor=1,1,1 SORTWhether to sort or not the PIV block=1,1,1 SWITCH1The switching functions parameter={RATIONAL R_0=1.4 NN=6 MM=12} SWITCH2The switching functions parameter={RATIONAL R_0=1.4 NN=6 MM=12} SWITCH3The switching functions parameter={RATIONAL R_0=1.4 NN=6 MM=12} NL_CUTOFFNeighbor lists cutoff=2.5,2.5,2.5 NL_STRIDEUpdate neighbor lists every NL_STRIDE steps=1,1,1 NL_SKINThe maximum atom displacement tolerated for the neighbor lists update=0.3,0.3,0.3 ... PIV
PIVCalculates the PIV-distance. More details ... LABELa label for the action so that its output can be referenced in the input to other actions=c2 PRECISIONthe precision for approximating reals with integers in sorting=1000 VOLUMEScale atom-atom distances by the cubic root of the cell volume=1 NLIST Use a neighbor list for distance calculations REF_FILEPDB file name that contains the ith reference structure=Crys.pdb PIVATOMSNumber of atoms to use for PIV=2 ATOMTYPESThe atom types to use for PIV=1,2 SFACTORScale the PIV-distance by such block-specific factor=1,1,1 SORTWhether to sort or not the PIV block=1,1,1 SWITCH1The switching functions parameter={RATIONAL R_0=1.4 NN=6 MM=12} SWITCH2The switching functions parameter={RATIONAL R_0=1.4 NN=6 MM=12} SWITCH3The switching functions parameter={RATIONAL R_0=1.4 NN=6 MM=12} NL_CUTOFFNeighbor lists cutoff=2.5,2.5,2.5 NL_STRIDEUpdate neighbor lists every NL_STRIDE steps=1,1,1 NL_SKINThe maximum atom displacement tolerated for the neighbor lists update=0.3,0.3,0.3 ... PIV # lambda*dist_ref1_ref2 = 2.3 p1: FUNCPATHMSDThis function calculates path collective variables. More details ARGthe labels of the values from which the function is calculated=c1,c2 LAMBDAthe lambda parameter is needed for smoothing, is in the units of plumed=4e-3 METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=s SIGMAthe widths of the Gaussian hills=0.04 HEIGHTthe heights of the Gaussian hills=0.1 PACEthe frequency for hill addition=1000 GRID_MINthe lower bounds for the grid=-15 GRID_MAXthe upper bounds for the grid=0 LABELa label for the action so that its output can be referenced in the input to other actions=res vol: VOLUMECalculate the volume the simulation box. More details UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=vol ATthe positions of the wall=3375 KAPPAthe force constant for the wall=1e3 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0 LABELa label for the action so that its output can be referenced in the input to other actions=uwall
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=p1.s,p1.z,s,e,uwall.bias,res.* STRIDE the frequency with which the quantities of interest should be output=2000 FILEthe name of the file on which to output these quantities=colvar.out FMTthe format that should be used to output real numbers=%15.6f