Project ID: plumID:20.031
Source: nanoshuttle_simulations/m16/plumed.dat
Originally used with PLUMED version: 2.7
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
#m16 #RESTARTWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More detailsSTRIDE=1the frequency with which molecules are reassembledENTITY0=1-3342the atoms that make up a molecule that you wish to alignENTITY1=3343-5951the atoms that make up a molecule that you wish to alignENTITY2=5952-8560the atoms that make up a molecule that you wish to alignENTITY3=8561-11169the atoms that make up a molecule that you wish to alignENTITY4=11170-13778the atoms that make up a molecule that you wish to alignENTITY5=13779-16387the atoms that make up a molecule that you wish to alignENTITY6=16388-18996the atoms that make up a molecule that you wish to alignENTITY7=18997-21605the atoms that make up a molecule that you wish to alignENTITY8=21606-24214the atoms that make up a molecule that you wish to alignENTITY9=24215-26823the atoms that make up a molecule that you wish to align
c1:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=2602,2600,2599,2605,2604 c2:the group of atoms that you are calculating the Gyration Tensor forCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=5296,5298,5299,5301,5306,5295 #d1: DISTANCE ATOMS=c1,c2the group of atoms that you are calculating the Gyration Tensor for
c3:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=2604,2605,2606,2608,2612,2610 c4:the group of atoms that you are calculating the Gyration Tensor forCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=5306,5301,5302,5303,5304,5305 #d2: DISTANCE ATOMS=c3,c4the group of atoms that you are calculating the Gyration Tensor for
c5:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=2602,2600,2599,2605,2604 c6:the group of atoms that you are calculating the Gyration Tensor forCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=10849,10851,10852,10854,10859,10848 #d3: DISTANCE ATOMS=c5,c6 # c7:the group of atoms that you are calculating the Gyration Tensor forCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=2604,2605,2606,2608,2612,2610 c8:the group of atoms that you are calculating the Gyration Tensor forCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=10859,10854,10855,10856,10857,10858 #d1: DISTANCE ATOMS=c7,c8the group of atoms that you are calculating the Gyration Tensor for
t1:COORDINATIONCalculate coordination numbers. More detailsGROUPA=1182,1183,1183,1182,2654,2654,1588,1527,2056,1182,1183,1183,1182,2654,2654,1588,1527,2056First list of atomsGROUPB=5295,5295,5297,5297,5298,5300,5300,5300,5302,10848,10848,10850,10850,10851,10853,10853,10853,10855Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.50The r_0 parameter of the switching functionPAIRt3:Pair only 1st element of the 1st group with 1st element in the second, etcCOORDINATIONCalculate coordination numbers. More detailsGROUPA=c1,c3,c5,c7First list of atomsGROUPB=c2,c4,c6,c8Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.60The r_0 parameter of the switching functionPAIRPair only 1st element of the 1st group with 1st element in the second, etcPBMETAD...Used to performed Parallel Bias metadynamics. More detailsLABEL=pba label for the action so that its output can be referenced in the input to other actionsARG=t1,t3the input for this action is the scalar output from one or more other actionsSIGMA=0.35,0.35the widths of the Gaussian hillsHEIGHT=1.2the height of the Gaussian hills, one for all biasesPACE=500the frequency for hill addition, one for all biasesFILE=HILLS_t1,HILLS_t3files in which the lists of added hills are stored, default names are assigned using arguments if FILE is not foundBIASFACTOR=25use well tempered metadynamics with this bias factor, one for all biasesTEMP=300the system temperature - this is only needed if you are doing well-tempered metadynamicsWALKERS_N=6number of walkersWALKERS_ID=0walker idWALKERS_DIRshared directory with the hills files from all the walkersWALKERS_RSTRIDE=500 ... PBMETADstride for reading hills filesPrint quantities to a file. More detailsARG=t1,t3,pb.biasthe input for this action is the scalar output from one or more other actionsSTRIDE=500the frequency with which the quantities of interest should be outputFILE=COLVARthe name of the file on which to output these quantities