**Project ID:** plumID:21.032

**Source:** plumed_PB_WTMetad.dat

**Originally used with PLUMED version:** 2.6

**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 detailsLENGTH=Athe units of lengthsENERGY=kcal/molthe units of energyWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More detailsENTITY0=1-774the atoms that make up a molecule that you wish to alignSTRIDE=1the frequency with which molecules are reassembledGROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More detailsATOMS=67,88,243,292the numerical indexes for the set of atoms in the groupLABEL=a label for the action so that its output can be referenced in the input to other actionscomCysZn69GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More detailsATOMS=152,88,324,173the numerical indexes for the set of atoms in the groupLABEL=a label for the action so that its output can be referenced in the input to other actionscomCysZn68GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More detailsATOMS=211,292,359,173the numerical indexes for the set of atoms in the groupLABEL=a label for the action so that its output can be referenced in the input to other actionscomCysZn67ATOMS=465,455,628,434the numerical indexes for the set of atoms in the groupLABEL=a label for the action so that its output can be referenced in the input to other actionscomCysZn66ATOMS=512,554,465,761the numerical indexes for the set of atoms in the groupLABEL=a label for the action so that its output can be referenced in the input to other actionscomCysZn65ATOMS=599,424,434,554the numerical indexes for the set of atoms in the groupLABEL=a label for the action so that its output can be referenced in the input to other actionscomCysZn64ATOMS=751,761,730,628the numerical indexes for the set of atoms in the groupLABEL=a label for the action so that its output can be referenced in the input to other actionscomCysZn63zn69:COORDINATIONCalculate coordination numbers. More detailsGROUPA=781First list of atomsGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)comCysZn69R_0=3.5The r_0 parameter of the switching functionNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=8The cutoff for the neighbor listNL_STRIDE=100The frequency with which we are updating the atoms in the neighbor listzn68:COORDINATIONCalculate coordination numbers. More detailsGROUPA=780First list of atomsGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)comCysZn68R_0=3.5The r_0 parameter of the switching functionNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=8The cutoff for the neighbor listNL_STRIDE=100The frequency with which we are updating the atoms in the neighbor listzn67:COORDINATIONCalculate coordination numbers. More detailsGROUPA=779First list of atomsGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)comCysZn67R_0=3.5The r_0 parameter of the switching functionNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=8The cutoff for the neighbor listNL_STRIDE=100The frequency with which we are updating the atoms in the neighbor listzn66:COORDINATIONCalculate coordination numbers. More detailsGROUPA=778First list of atomsGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)comCysZn66R_0=3.5The r_0 parameter of the switching functionNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=8The cutoff for the neighbor listNL_STRIDE=100The frequency with which we are updating the atoms in the neighbor listzn65:COORDINATIONCalculate coordination numbers. More detailsGROUPA=777First list of atomsGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)comCysZn65R_0=3.5The r_0 parameter of the switching functionNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=8The cutoff for the neighbor listNL_STRIDE=100The frequency with which we are updating the atoms in the neighbor listzn64:COORDINATIONCalculate coordination numbers. More detailsGROUPA=776First list of atomsGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)comCysZn64R_0=3.5The r_0 parameter of the switching functionNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=8The cutoff for the neighbor listNL_STRIDE=100The frequency with which we are updating the atoms in the neighbor listzn63:COORDINATIONCalculate coordination numbers. More detailsGROUPA=775First list of atomsGROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)comCysZn63R_0=3.5The r_0 parameter of the switching functionNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=8The cutoff for the neighbor listNL_STRIDE=100The frequency with which we are updating the atoms in the neighbor listPBMETAD...Used to performed Parallel Bias metadynamics. More detailsARG=the input for this action is the scalar output from one or more other actionszn69,zn68,zn67,zn66,zn65,zn64,zn63PACE=500the frequency for hill addition, one for all biasesBIASFACTOR=18.0use well tempered metadynamics with this bias factor, one for all biasesHEIGHT=0.6the height of the Gaussian hills, one for all biasesTEMP=300.0the system temperature - this is only needed if you are doing well-tempered metadynamicsINTERVAL_MIN=0.4,0.4,0.4,0.4,0.4,0.4,0.4one dimensional lower limits, outside the limits the system will not feel the biasing forceINTERVAL_MAX=4,4,4,4,4,4,4one dimensional upper limits, outside the limits the system will not feel the biasing forceSIGMA=0.15,0.15,0.15,0.15,0.15,0.15,0.15the widths of the Gaussian hillsGRID_MIN=0,0,0,0,0,0,0the lower bounds for the gridGRID_MAX=30,30,30,30,30,30,30the upper bounds for the gridWALKERS_MPISwitch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIRFILE=HILLS_69,HILLS_68,HILLS_67,HILLS_66,HILLS_65,HILLS_64,HILLS_63files in which the lists of added hills are stored, default names are assigned using arguments if FILE is not foundLABEL=a label for the action so that its output can be referenced in the input to other actionsmetad... PBMETAD