Project ID: plumID:21.015
Source: MetaD/CBM5/plumed.dat
Originally used with PLUMED version: 2.5
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
#RESTARTWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More detailsENTITY0=721-887the atoms that make up a molecule that you wish to align
a1:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=798-801 a2:the group of atoms that you are calculating the Gyration Tensor forCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=803-807 a3:the group of atoms that you are calculating the Gyration Tensor forCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=832-835 achi:the group of atoms that you are calculating the Gyration Tensor forCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1-720the group of atoms that you are calculating the Gyration Tensor for
p1:POSITIONCalculate the components of the position of an atom. More detailsATOM=a1the atom numberNOPBCp2:ignore the periodic boundary conditions when calculating distancesPOSITIONCalculate the components of the position of an atom. More detailsATOM=a2the atom numberNOPBCp3:ignore the periodic boundary conditions when calculating distancesPOSITIONCalculate the components of the position of an atom. More detailsATOM=a3the atom numberNOPBCpchi:ignore the periodic boundary conditions when calculating distancesPOSITIONCalculate the components of the position of an atom. More detailsATOM=achithe atom numberNOPBCignore the periodic boundary conditions when calculating distances
c:COORDINATIONCalculate coordination numbers. More detailsGROUPA=798-801,803-807,832-835First list of atomsGROUPB=1-720Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.7The cutoff for the neighbor listNL_STRIDE=100 distx:The frequency with which we are updating the atoms in the neighbor listMATHEVALAn alias to the ef CUSTOM function. More detailsARG=p1.x,p2.x,p3.x,pchi.xthe input to this functionVAR=a,b,c,ythe names to give each of the arguments in the functionFUNC=((y-a)^2+(y-b)^2+(y-c)^2)^0.5the function you wish to evaluatePERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionMETAD...Used to performed metadynamics on one or more collective variables. More detailsARG=c,distxthe input for this action is the scalar output from one or more other actionsSIGMA=0.5,0.5the widths of the Gaussian hillsHEIGHT=2.0the heights of the Gaussian hillsTEMP=300the system temperature - this is only needed if you are doing well-tempered metadynamicsPACE=500the frequency for hill additionBIASFACTOR=50.0use well tempered metadynamics and use this bias factorFILE=HILLSa file in which the list of added hills is storedGRID_MIN=0.0,0.0the lower bounds for the gridGRID_MAX=75.0,35.0the upper bounds for the gridGRID_BIN=375,175the number of bins for the gridLABEL=metad ... METADa label for the action so that its output can be referenced in the input to other actionsPrint quantities to a file. More detailsARG=c,distx,metad.biasthe input for this action is the scalar output from one or more other actionsSTRIDE=5000the frequency with which the quantities of interest should be outputFILE=COLVARthe name of the file on which to output these quantities