Project ID: plumID:23.002
Source: 1_Metadynamics/4_Q6/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
#########UNITSThis command sets the internal units for the code. More detailsNATURALuse natural units
q6:Q6Calculate sixth order Steinhardt parameters. More detailsSPECIES=1-4394this keyword is used for colvars such as coordination numberSWITCH={GAUSSIAN D_0=1.37 R_0=0.1 D_MAX=1.4}the switching function that it used in the construction of the contact matrixMEANcalculate the mean of all the quantitiesLOWMEMaq6:this flag does nothing and is present only to ensure back-compatibilityLOCAL_AVERAGECalculate averages over spherical regions centered on atoms More detailsSPECIES=q6this keyword is used for colvars such as coordination numberSWITCH={GAUSSIAN D_0=1.37 R_0=0.1 D_MAX=1.4}the switching function that it used in the construction of the contact matrixMORE_THAN1={SMAP R_0=0.25 D_0=0.0 A=8 B=8} LOWMEMcalculate the number of variables that are more than a certain target value
vol:VOLUMECalculate the volume of the simulation box. More detailsUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=volthe arguments on which the bias is actingAT=3375the positions of the wallKAPPA=1e3the force constant for the wallEXP=2the powers for the wallsEPS=1the values for s_i in the expression for a wallOFFSET=0the offset for the start of the wallLABEL=uwalla label for the action so that its output can be referenced in the input to other actions
ene:ENERGYe:Calculate the total potential energy of the simulation box. More detailsCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=enethe input to this functionFUNC=x/4394.0the function you wish to evaluatePERIODIC=NO s:if the output of your function is periodic then you should specify the periodicity of the functionPAIRENTROPYATOMS=1-4394Calculate the KL Entropy from the radial distribution function More detailsMAXR=2.5 SIGMA=0.05 NLIST NL_CUTOFF=2.8 NL_STRIDE=10the maximum distance to use for the rdfPIV...Calculates the PIV-distance. More detailsLABEL=c1a label for the action so that its output can be referenced in the input to other actionsPRECISION=1000the precision for approximating reals with integers in sortingVOLUME=1Scale atom-atom distances by the cubic root of the cell volumeNLISTUse a neighbor list for distance calculationsREF_FILE=Liq.pdbPDB file name that contains the $i$th reference structurePIVATOMS=2Number of atoms to use for PIVATOMTYPES=1,2The atom types to use for PIVSFACTOR=1,1,1Scale the PIV-distance by such block-specific factorSORT=1,1,1Whether to sort or not the PIV blockSWITCH1={RATIONAL R_0=1.4 NN=6 MM=12}The switching functions parameterSWITCH2={RATIONAL R_0=1.4 NN=6 MM=12}The switching functions parameterSWITCH3={RATIONAL R_0=1.4 NN=6 MM=12}The switching functions parameterNL_CUTOFF=2.5,2.5,2.5Neighbor lists cutoffNL_STRIDE=1,1,1Update neighbor lists every NL_STRIDE stepsNL_SKIN=0.3,0.3,0.3 ... PIVThe maximum atom displacement tolerated for the neighbor lists updatePIV...Calculates the PIV-distance. More detailsLABEL=c2a label for the action so that its output can be referenced in the input to other actionsPRECISION=1000the precision for approximating reals with integers in sortingVOLUME=1Scale atom-atom distances by the cubic root of the cell volumeNLISTUse a neighbor list for distance calculationsREF_FILE=Crys.pdbPDB file name that contains the $i$th reference structurePIVATOMS=2Number of atoms to use for PIVATOMTYPES=1,2The atom types to use for PIVSFACTOR=1,1,1Scale the PIV-distance by such block-specific factorSORT=1,1,1Whether to sort or not the PIV blockSWITCH1={RATIONAL R_0=1.4 NN=6 MM=12}The switching functions parameterSWITCH2={RATIONAL R_0=1.4 NN=6 MM=12}The switching functions parameterSWITCH3={RATIONAL R_0=1.4 NN=6 MM=12}The switching functions parameterNL_CUTOFF=2.5,2.5,2.5Neighbor lists cutoffNL_STRIDE=1,1,1Update neighbor lists every NL_STRIDE stepsNL_SKIN=0.3,0.3,0.3 ... PIV # lambda*dist_ref1_ref2 = 2.3 p1:The maximum atom displacement tolerated for the neighbor lists updateFUNCPATHMSDThis function calculates path collective variables. More detailsARG=c1,c2the input for this action is the scalar output from one or more other actionsLAMBDA=4e-3the lambda parameter is needed for smoothing, is in the units of plumedMETADUsed to performed metadynamics on one or more collective variables. More detailsARG=aq6.morethan-1the input for this action is the scalar output from one or more other actionsSIGMA=3the widths of the Gaussian hillsHEIGHT=0.5the heights of the Gaussian hillsPACE=1000the frequency for hill additionLABEL=res #METAD ARG=aq6. SIGMA=0.008 HEIGHT=0.05 PACE=1000 GRID_MIN=0.9 GRID_MAX=2.1 RESTART=YES LABEL=resa label for the action so that its output can be referenced in the input to other actionsPrint quantities to a file. More detailsARG=p1.s,p1.z,s,e,uwall.bias,res.*,aq6the input for this action is the scalar output from one or more other actionsSTRIDE=1000the frequency with which the quantities of interest should be outputFILE=colvar.outthe name of the file on which to output these quantitiesFMT=%15.6fthe format that should be used to output real numbers