Project ID: plumID:21.032
Source: plumed_reweight.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=comCysZn69a label for the action so that its output can be referenced in the input to other actionsGROUPDefine 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=comCysZn68a label for the action so that its output can be referenced in the input to other actionsGROUPDefine 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=comCysZn67a label for the action so that its output can be referenced in the input to other actionsGROUPDefine 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=465,455,628,434the numerical indexes for the set of atoms in the groupLABEL=comCysZn66a label for the action so that its output can be referenced in the input to other actionsGROUPDefine 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=512,554,465,761the numerical indexes for the set of atoms in the groupLABEL=comCysZn65a label for the action so that its output can be referenced in the input to other actionsGROUPDefine 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=599,424,434,554the numerical indexes for the set of atoms in the groupLABEL=comCysZn64a label for the action so that its output can be referenced in the input to other actionsGROUPDefine 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=751,761,730,628the numerical indexes for the set of atoms in the groupLABEL=comCysZn63a label for the action so that its output can be referenced in the input to other actions
zn69COORDINATIONCalculate coordination numbers. This action has hidden defaults. More detailsGROUPA=781First list of atomsGROUPB=comCysZn69Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_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=100 : zn68The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. This action has hidden defaults. More detailsGROUPA=780First list of atomsGROUPB=comCysZn68Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_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=100 : zn67The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. This action has hidden defaults. More detailsGROUPA=779First list of atomsGROUPB=comCysZn67Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_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=100 : zn66The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. This action has hidden defaults. More detailsGROUPA=778First list of atomsGROUPB=comCysZn66Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_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=100 : zn65The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. This action has hidden defaults. More detailsGROUPA=777First list of atomsGROUPB=comCysZn65Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_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=100 : zn64The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. This action has hidden defaults. More detailsGROUPA=776First list of atomsGROUPB=comCysZn64Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_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=100 : zn63The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. This action has hidden defaults. More detailsGROUPA=775First list of atomsGROUPB=comCysZn63Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_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=100 :The frequency with which we are updating the atoms in the neighbor listPBMETAD...Used to performed Parallel Bias metadynamics. More detailsARG=zn69,zn68,zn67,zn66,zn65,zn64,zn63the input for this action is the scalar output from one or more other actionsPACE=10000000the frequency for hill addition, one for all biasesHEIGHT=0.0the height of the Gaussian hills, one for all biasesBIASFACTOR=18.0use well tempered metadynamics with this bias factor, one for all biasesTEMP=300.0the system temperature - this is only needed if you are doing well-tempered metadynamicsSIGMA=0.15,0.15,0.15,0.15,0.15,0.15,0.15the widths of the Gaussian hillsGRID_MIN=0.,0.0,0.0,0.0,0.0,0.0,0the lower bounds for the gridGRID_MAX=30,30,30,30,30,30,30the upper bounds for the gridFILE=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=metada label for the action so that its output can be referenced in the input to other actionsRESTART=YES ... PBMETADallows per-action setting of restart (YES/NO/AUTO)Print quantities to a file. More detailsARG=zn69,zn68,zn67,zn66,zn65,zn64,zn63,metad.biasthe input for this action is the scalar output from one or more other actionsFILE=COLVAR_REWEIGHT_3the name of the file on which to output these quantitiesSTRIDE=1the frequency with which the quantities of interest should be output