Project ID: plumID:21.003
Source: metainf_input/plumed.dat
Originally used with PLUMED version: 2.4
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
#SETTINGS NREPLICAS=2 # M&M plumed input fileMOLINFOThis command is used to provide information on the molecules that are present in your system. More detailsMOLTYPE=proteinwhat kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatibleSTRUCTURE=master.pdba file in pdb format containing a reference structureWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More detailsENTITY0=1-2016the atoms that make up a molecule that you wish to align
protein-h:GROUPDefine 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 detailsNDX_FILE=index.ndxthe name of index file (gromacs syntax)NDX_GROUP=Protein-H solv:the name of the group to be imported (gromacs syntax) - first group found is used by defaultEEFSOLVCalculates EEF1 solvation free energy for a group of atoms. More detailsATOMS=protein-hThe atoms to be included in the calculation, eNL_STRIDE=20The frequency with which the neighbor list is updatedNL_BUFFER=0.1 Sbias:The buffer to the intrinsic cutoff used when calculating pairwise interactionsBIASVALUETakes the value of one variable and use it as a bias More detailsARG=solvthe input for this action is the scalar output from one or more other actionsPrint quantities to a file. More detailsARG=solvthe input for this action is the scalar output from one or more other actionsFILE=SOLVthe name of the file on which to output these quantities
bead1:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1,2,3,4,5,18,19the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,1,1,1,12,12,16what weights should be used when calculating the centerNOPBCbead2:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=7,10,13,14the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,32,12what weights should be used when calculating the centerNOPBCbead3:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=20,22,30,31the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead4:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=24,27,28,29the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,16,16what weights should be used when calculating the centerNOPBCbead5:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=32,34,46,47the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead6:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=36,38,42the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12what weights should be used when calculating the centerNOPBCbead7:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=48,50,66,67the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead8:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=52,55,56,57the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12,1what weights should be used when calculating the centerNOPBCbead9:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=62,63,64,65the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,1,12,1what weights should be used when calculating the centerNOPBCbead10:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=58,59,60,61the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,1,12,1what weights should be used when calculating the centerNOPBCbead11:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=68,70,83,84the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead12:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=72,75,78,79the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,32,12what weights should be used when calculating the centerNOPBCbead13:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=85,87,105,106the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead14:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=89,92,95the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12what weights should be used when calculating the centerNOPBCbead15:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=98,101,102,103,104the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,14,1,1,1what weights should be used when calculating the centerNOPBCbead16:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=107,109,112,113the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead17:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=114,116,131,132the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead18:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=118,121,123,127the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12,12what weights should be used when calculating the centerNOPBCbead19:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=133,135,142,143the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead20:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=137,140the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,16what weights should be used when calculating the centerNOPBCbead21:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=144,146,164,165the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead22:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=148,151,154the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12what weights should be used when calculating the centerNOPBCbead23:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=157,160,161,162,163the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,14,1,1,1what weights should be used when calculating the centerNOPBCbead24:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=166,168,170,174,175the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,12,16what weights should be used when calculating the centerNOPBCbead25:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=176,178,196,197the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead26:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=180,183,186the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12what weights should be used when calculating the centerNOPBCbead27:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=189,192,193,194,195the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,14,1,1,1what weights should be used when calculating the centerNOPBCbead28:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=198,200,211,212the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead29:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=202,205,208,209,210the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12,16,16what weights should be used when calculating the centerNOPBCbead30:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=213,215,218,219the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead31:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=220,222,234,235the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead32:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=224,226,230the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12what weights should be used when calculating the centerNOPBCbead33:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=236,238,250,251the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead34:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=240,242,246the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12what weights should be used when calculating the centerNOPBCbead35:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=252,254,256,260,261the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,12,16what weights should be used when calculating the centerNOPBCbead36:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=262,264,266,270,271the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,12,16what weights should be used when calculating the centerNOPBCbead37:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=272,274,276,280,281the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,12,16what weights should be used when calculating the centerNOPBCbead38:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=282,284,295,296the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead39:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=286,289,292,293,294the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12,16,16what weights should be used when calculating the centerNOPBCbead40:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=297,299,317,318the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead41:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=301,304,307the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12what weights should be used when calculating the centerNOPBCbead42:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=310,313,314,315,316the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,14,1,1,1what weights should be used when calculating the centerNOPBCbead43:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=319,321,331,332the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead44:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=323,325,326,327the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,16,1,12what weights should be used when calculating the centerNOPBCbead45:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=333,335,353,354the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead46:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=337,340,343the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12what weights should be used when calculating the centerNOPBCbead47:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=346,349,350,351,352the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,14,1,1,1what weights should be used when calculating the centerNOPBCbead48:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=355,357,370,371the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead49:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=359,362,365,366,367the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12,16,14what weights should be used when calculating the centerNOPBCbead50:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=372,374,377,378the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead51:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=379,381,393,394the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead52:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=383,385,389the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12what weights should be used when calculating the centerNOPBCbead53:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=395,397,399,403,404the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,12,16what weights should be used when calculating the centerNOPBCbead54:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=405,407,418,419the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead55:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=409,412,415,416,417the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12,16,16what weights should be used when calculating the centerNOPBCbead56:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=420,422,424,428,429the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,12,16what weights should be used when calculating the centerNOPBCbead57:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=430,432,434,438,439the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,12,16what weights should be used when calculating the centerNOPBCbead58:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=440,442,445,446the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead59:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=447,449,467,468the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead60:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=451,454,457the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12what weights should be used when calculating the centerNOPBCbead61:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=460,463,464,465,466the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,14,1,1,1what weights should be used when calculating the centerNOPBCbead62:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=469,471,481,482the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead63:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=473,475,476,477the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,16,1,12what weights should be used when calculating the centerNOPBCbead64:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=483,485,503,504the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead65:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=487,490,493the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12what weights should be used when calculating the centerNOPBCbead66:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=496,499,500,501,502the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,14,1,1,1what weights should be used when calculating the centerNOPBCbead67:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=505,507,518,519the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead68:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=509,512,515,516,517the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12,16,16what weights should be used when calculating the centerNOPBCbead69:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=520,522,525,526the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead70:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=527,529,541,542the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead71:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=531,533,537the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12what weights should be used when calculating the centerNOPBCbead72:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=543,545,560,561the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead73:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=547,550,552,556the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12,12what weights should be used when calculating the centerNOPBCbead74:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=562,564,581,582the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead75:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=566,569,570,571the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12,1what weights should be used when calculating the centerNOPBCbead76:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=577,578,579,580the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,1,12,1what weights should be used when calculating the centerNOPBCbead77:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=572,573,574,575,576the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,1,12,16,1what weights should be used when calculating the centerNOPBCbead78:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=583,585,597,598the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead79:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=587,589,593the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12what weights should be used when calculating the centerNOPBCbead80:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=599,601,604,605the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead81:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=606,608,615,616the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead82:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=610,613the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,16what weights should be used when calculating the centerNOPBCbead83:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=617,619,637,638the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead84:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=621,624,627the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12what weights should be used when calculating the centerNOPBCbead85:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=630,633,634,635,636the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,14,1,1,1what weights should be used when calculating the centerNOPBCbead86:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=639,641,651,652the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead87:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=643,645,646,647the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,16,1,12what weights should be used when calculating the centerNOPBCbead88:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=653,655,673,674the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead89:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=657,660,663the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12what weights should be used when calculating the centerNOPBCbead90:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=666,669,670,671,672the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,14,1,1,1what weights should be used when calculating the centerNOPBCbead91:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=675,677,688,689the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead92:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=679,682,685,686,687the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12,16,16what weights should be used when calculating the centerNOPBCbead93:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=690,692,695,696the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead94:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=697,699,711,712the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead95:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=701,703,707the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12what weights should be used when calculating the centerNOPBCbead96:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=713,715,727,728the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead97:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=717,719,723the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12what weights should be used when calculating the centerNOPBCbead98:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=729,731,744,745the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead99:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=733,737the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12what weights should be used when calculating the centerNOPBCbead100:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=740,741,742,743the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,1,12,1what weights should be used when calculating the centerNOPBCbead101:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=736,738,739the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,1what weights should be used when calculating the centerNOPBCbead102:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=746,748,751,752the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead103:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=753,755,767,768the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead104:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=757,759,763the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12what weights should be used when calculating the centerNOPBCbead105:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=769,771,773,777,778the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,12,16what weights should be used when calculating the centerNOPBCbead106:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=779,781,791,792the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead107:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=783,785,786,787the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,16,1,12what weights should be used when calculating the centerNOPBCbead108:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=793,795,807,808the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead109:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=797,799,803the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12what weights should be used when calculating the centerNOPBCbead110:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=809,811,813,817,818the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,12,16what weights should be used when calculating the centerNOPBCbead111:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=819,821,832,833the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead112:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=823,826,829,830,831the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12,16,16what weights should be used when calculating the centerNOPBCbead113:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=834,836,854,855the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead114:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=838,841,844the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12what weights should be used when calculating the centerNOPBCbead115:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=847,850,851,852,853the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,14,1,1,1what weights should be used when calculating the centerNOPBCbead116:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=856,858,868,869the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead117:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=860,862,863,864the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,16,1,12what weights should be used when calculating the centerNOPBCbead118:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=870,872,890,891the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead119:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=874,877,880the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12what weights should be used when calculating the centerNOPBCbead120:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=883,886,887,888,889the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,14,1,1,1what weights should be used when calculating the centerNOPBCbead121:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=892,894,905,906the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead122:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=896,899,902,903,904the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12,16,16what weights should be used when calculating the centerNOPBCbead123:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=907,909,922,923the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead124:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=911,914,917,918,919the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12,16,14what weights should be used when calculating the centerNOPBCbead125:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=924,926,938,939the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead126:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=928,930,934the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12what weights should be used when calculating the centerNOPBCbead127:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=940,942,952,953the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead128:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=944,946,947,948the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,16,1,12what weights should be used when calculating the centerNOPBCbead129:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=954,956,966,967the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead130:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=958,961,962,963the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,16,14what weights should be used when calculating the centerNOPBCbead131:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=968,970,982,983the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead132:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=972,974,978the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12what weights should be used when calculating the centerNOPBCbead133:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=984,986,989,990the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead134:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=991,993,996,997the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead135:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=998,1000,1002,1006,1007the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,12,16what weights should be used when calculating the centerNOPBCbead136:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1008,1010,1022,1023the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead137:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1012,1014,1018the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12what weights should be used when calculating the centerNOPBCbead138:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1024,1026,1038,1039the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead139:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1028,1030,1034the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12what weights should be used when calculating the centerNOPBCbead140:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1040,1042,1052,1053the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead141:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1044,1046,1047,1048the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,16,1,12what weights should be used when calculating the centerNOPBCbead142:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1054,1056,1059,1060the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead143:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1061,1063,1075,1076the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead144:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1065,1067,1071the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12what weights should be used when calculating the centerNOPBCbead145:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1077,1079,1089,1090the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead146:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1081,1083,1084,1085the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,16,1,12what weights should be used when calculating the centerNOPBCbead147:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1091,1093,1095,1099,1100the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,12,16what weights should be used when calculating the centerNOPBCbead148:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1101,1103,1115,1116the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead149:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1105,1107,1111the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12what weights should be used when calculating the centerNOPBCbead150:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1117,1119,1121,1125,1126the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,12,16what weights should be used when calculating the centerNOPBCbead151:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1127,1129,1142,1143the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead152:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1131,1134,1137,1138,1139the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12,16,14what weights should be used when calculating the centerNOPBCbead153:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1144,1146,1164,1165the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead154:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1148,1151,1154the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12what weights should be used when calculating the centerNOPBCbead155:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1157,1160,1161,1162,1163the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,14,1,1,1what weights should be used when calculating the centerNOPBCbead156:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1166,1168,1178,1179the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead157:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1170,1172,1173,1174the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,16,1,12what weights should be used when calculating the centerNOPBCbead158:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1180,1182,1194,1195the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead159:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1184,1186,1190the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12what weights should be used when calculating the centerNOPBCbead160:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1196,1198,1209,1210the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead161:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1200,1203,1206,1207,1208the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12,16,16what weights should be used when calculating the centerNOPBCbead162:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1211,1213,1216,1217the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead163:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1218,1220,1222,1226,1227the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,12,16what weights should be used when calculating the centerNOPBCbead164:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1228,1230,1233,1234the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead165:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1235,1237,1244,1245the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead166:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1239,1242the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,16what weights should be used when calculating the centerNOPBCbead167:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1246,1248,1263,1264the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead168:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1250,1252,1256,1259the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12,12what weights should be used when calculating the centerNOPBCbead169:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1265,1267,1269,1273,1274the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,12,16what weights should be used when calculating the centerNOPBCbead170:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1275,1277,1279,1283,1284the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,12,16what weights should be used when calculating the centerNOPBCbead171:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1285,1287,1289,1293,1294the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,12,16what weights should be used when calculating the centerNOPBCbead172:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1295,1297,1307,1308the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead173:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1299,1301,1302,1303the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,16,1,12what weights should be used when calculating the centerNOPBCbead174:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1309,1311,1314,1315the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead175:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1316,1318,1334,1335the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead176:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1320,1323,1324,1325the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12,1what weights should be used when calculating the centerNOPBCbead177:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1330,1331,1332,1333the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,1,12,1what weights should be used when calculating the centerNOPBCbead178:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1326,1327,1328,1329the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,1,12,1what weights should be used when calculating the centerNOPBCbead179:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1336,1338,1350,1351the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead180:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1340,1342,1346the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12what weights should be used when calculating the centerNOPBCbead181:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1352,1354,1372,1373the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead182:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1356,1359,1362the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12what weights should be used when calculating the centerNOPBCbead183:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1365,1368,1369,1370,1371the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,14,1,1,1what weights should be used when calculating the centerNOPBCbead184:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1374,1376,1394,1395the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead185:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1378,1381,1384the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12what weights should be used when calculating the centerNOPBCbead186:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1387,1390,1391,1392,1393the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,14,1,1,1what weights should be used when calculating the centerNOPBCbead187:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1396,1398,1406,1407the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead188:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1400,1403,1404,1405the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,16,16what weights should be used when calculating the centerNOPBCbead189:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1408,1410,1423,1424the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead190:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1412,1415,1418,1419,1420the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12,16,14what weights should be used when calculating the centerNOPBCbead191:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1425,1427,1442,1443the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead192:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1429,1432,1434,1438the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12,12what weights should be used when calculating the centerNOPBCbead193:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1444,1446,1449,1450the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead194:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1451,1453,1471,1472the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead195:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1455,1458,1461the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12what weights should be used when calculating the centerNOPBCbead196:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1464,1467,1468,1469,1470the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,14,1,1,1what weights should be used when calculating the centerNOPBCbead197:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1473,1475,1485,1486the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead198:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1477,1480,1481,1482the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,16,14what weights should be used when calculating the centerNOPBCbead199:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1487,1489,1500,1501the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead200:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1491,1494,1497,1498,1499the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12,16,16what weights should be used when calculating the centerNOPBCbead201:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1502,1504,1515,1516the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead202:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1506,1509,1512,1513,1514the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12,16,16what weights should be used when calculating the centerNOPBCbead203:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1517,1519,1522,1523the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead204:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1524,1526,1528,1532,1533the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,12,16what weights should be used when calculating the centerNOPBCbead205:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1534,1538,1546,1547the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead206:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1535,1540,1543the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12what weights should be used when calculating the centerNOPBCbead207:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1548,1550,1563,1564the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead208:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1552,1555,1558,1559,1560the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12,16,14what weights should be used when calculating the centerNOPBCbead209:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1565,1567,1578,1579the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead210:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1569,1572,1575,1576,1577the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12,16,16what weights should be used when calculating the centerNOPBCbead211:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1580,1582,1585,1586the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead212:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1587,1589,1604,1605the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead213:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1591,1593,1597,1600the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12,12what weights should be used when calculating the centerNOPBCbead214:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1606,1608,1623,1624the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead215:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1610,1613,1615,1619the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12,12what weights should be used when calculating the centerNOPBCbead216:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1625,1627,1638,1639the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead217:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1629,1632,1635,1636,1637the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12,16,16what weights should be used when calculating the centerNOPBCbead218:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1640,1642,1650,1651the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead219:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1644,1647,1648,1649the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,16,16what weights should be used when calculating the centerNOPBCbead220:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1652,1654,1667,1668the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead221:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1656,1659,1662,1663the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,32,12what weights should be used when calculating the centerNOPBCbead222:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1669,1673,1681,1682the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead223:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1670,1675,1678the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12what weights should be used when calculating the centerNOPBCbead224:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1683,1685,1697,1698the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead225:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1687,1689,1693the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12what weights should be used when calculating the centerNOPBCbead226:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1699,1701,1709,1710the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead227:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1703,1706,1707,1708the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,16,16what weights should be used when calculating the centerNOPBCbead228:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1711,1715,1723,1724the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead229:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1712,1717,1720the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12what weights should be used when calculating the centerNOPBCbead230:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1725,1727,1735,1736the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead231:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1729,1732,1733,1734the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,16,16what weights should be used when calculating the centerNOPBCbead232:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1737,1739,1749,1750the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead233:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1741,1744,1745,1746the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,16,14what weights should be used when calculating the centerNOPBCbead234:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1751,1753,1764,1765the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead235:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1755,1758,1761,1762,1763the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12,16,16what weights should be used when calculating the centerNOPBCbead236:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1766,1768,1770,1774,1775the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,12,16what weights should be used when calculating the centerNOPBCbead237:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1776,1778,1795,1796the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead238:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1780,1783,1784,1785the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12,1what weights should be used when calculating the centerNOPBCbead239:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1791,1792,1793,1794the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,1,12,1what weights should be used when calculating the centerNOPBCbead240:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1786,1787,1788,1789,1790the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,1,12,16,1what weights should be used when calculating the centerNOPBCbead241:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1797,1799,1810,1811the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead242:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1801,1804,1807,1808,1809the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12,16,16what weights should be used when calculating the centerNOPBCbead243:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1812,1814,1827,1828the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead244:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1816,1819,1822,1823the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,32,12what weights should be used when calculating the centerNOPBCbead245:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1829,1833,1841,1842the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead246:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1830,1835,1838the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12what weights should be used when calculating the centerNOPBCbead247:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1843,1845,1852,1853the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead248:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1847,1850the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,16what weights should be used when calculating the centerNOPBCbead249:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1854,1856,1867,1868the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead250:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1858,1861,1864,1865,1866the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12,16,16what weights should be used when calculating the centerNOPBCbead251:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1869,1871,1882,1883the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead252:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1873,1876,1879,1880,1881the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12,16,16what weights should be used when calculating the centerNOPBCbead253:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1884,1886,1889,1890the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead254:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1891,1893,1910,1911the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead255:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1895,1898,1899,1900the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12,1what weights should be used when calculating the centerNOPBCbead256:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1906,1907,1908,1909the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,1,12,1what weights should be used when calculating the centerNOPBCbead257:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1901,1902,1903,1904,1905the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,1,12,16,1what weights should be used when calculating the centerNOPBCbead258:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1912,1914,1927,1928the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead259:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1916,1919,1922,1923,1924the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12,16,14what weights should be used when calculating the centerNOPBCbead260:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1929,1931,1939,1940the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead261:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1933,1936,1937,1938the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,16,16what weights should be used when calculating the centerNOPBCbead262:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1941,1943,1960,1961the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead263:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1945,1948,1949,1950the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12,1what weights should be used when calculating the centerNOPBCbead264:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1956,1957,1958,1959the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,1,12,1what weights should be used when calculating the centerNOPBCbead265:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1951,1952,1953,1954,1955the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,1,12,16,1what weights should be used when calculating the centerNOPBCbead266:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1962,1964,1975,1976the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead267:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1966,1969,1972,1973,1974the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12,16,16what weights should be used when calculating the centerNOPBCbead268:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1977,1981,1989,1990the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead269:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1978,1983,1986the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12what weights should be used when calculating the centerNOPBCbead270:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1991,1993,2004,2005the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,16what weights should be used when calculating the centerNOPBCbead271:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1995,1998,2001,2002,2003the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=12,12,12,16,16what weights should be used when calculating the centerNOPBCbead272:ignore the periodic boundary conditions when calculating distancesCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=2006,2008,2010,2014the group of atoms that you are calculating the Gyration Tensor forWEIGHTS=14,12,12,12what weights should be used when calculating the centerNOPBCignore the periodic boundary conditions when calculating distances
#MetaD CVsALPHARMSD...Probe the alpha helical content of a protein structure. More detailsRESIDUES=1-6this command is used to specify the set of residues that could conceivably form part of the secondary structureTYPE=OPTIMALthe manner in which RMSD alignment is performedLESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12}calculate the number of a residue segments that are within a certain target distance of this secondary structure typeLABEL=ab1 ... ALPHARMSDa label for the action so that its output can be referenced in the input to other actionsALPHARMSD...Probe the alpha helical content of a protein structure. More detailsRESIDUES=7-12this command is used to specify the set of residues that could conceivably form part of the secondary structureTYPE=OPTIMALthe manner in which RMSD alignment is performedLESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12}calculate the number of a residue segments that are within a certain target distance of this secondary structure typeLABEL=ab2 ... ALPHARMSDa label for the action so that its output can be referenced in the input to other actionsALPHARMSD...Probe the alpha helical content of a protein structure. More detailsRESIDUES=13-18this command is used to specify the set of residues that could conceivably form part of the secondary structureTYPE=OPTIMALthe manner in which RMSD alignment is performedLESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12}calculate the number of a residue segments that are within a certain target distance of this secondary structure typeLABEL=ab3 ... ALPHARMSDa label for the action so that its output can be referenced in the input to other actionsALPHARMSD...Probe the alpha helical content of a protein structure. More detailsRESIDUES=19-24this command is used to specify the set of residues that could conceivably form part of the secondary structureTYPE=OPTIMALthe manner in which RMSD alignment is performedLESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12}calculate the number of a residue segments that are within a certain target distance of this secondary structure typeLABEL=ab4 ... ALPHARMSDa label for the action so that its output can be referenced in the input to other actionsALPHARMSD...Probe the alpha helical content of a protein structure. More detailsRESIDUES=25-30this command is used to specify the set of residues that could conceivably form part of the secondary structureTYPE=OPTIMALthe manner in which RMSD alignment is performedLESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12}calculate the number of a residue segments that are within a certain target distance of this secondary structure typeLABEL=ab5 ... ALPHARMSDa label for the action so that its output can be referenced in the input to other actionsALPHARMSD...Probe the alpha helical content of a protein structure. More detailsRESIDUES=26-36this command is used to specify the set of residues that could conceivably form part of the secondary structureTYPE=OPTIMALthe manner in which RMSD alignment is performedLESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12}calculate the number of a residue segments that are within a certain target distance of this secondary structure typeLABEL=ab6 ... ALPHARMSDa label for the action so that its output can be referenced in the input to other actionsALPHARMSD...Probe the alpha helical content of a protein structure. More detailsRESIDUES=37-42this command is used to specify the set of residues that could conceivably form part of the secondary structureTYPE=OPTIMALthe manner in which RMSD alignment is performedLESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12}calculate the number of a residue segments that are within a certain target distance of this secondary structure typeLABEL=ab7 ... ALPHARMSDa label for the action so that its output can be referenced in the input to other actionsALPHARMSD...Probe the alpha helical content of a protein structure. More detailsRESIDUES=43-48this command is used to specify the set of residues that could conceivably form part of the secondary structureTYPE=OPTIMALthe manner in which RMSD alignment is performedLESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12}calculate the number of a residue segments that are within a certain target distance of this secondary structure typeLABEL=ab8 ... ALPHARMSDa label for the action so that its output can be referenced in the input to other actionsALPHARMSD...Probe the alpha helical content of a protein structure. More detailsRESIDUES=49-54this command is used to specify the set of residues that could conceivably form part of the secondary structureTYPE=OPTIMALthe manner in which RMSD alignment is performedLESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12}calculate the number of a residue segments that are within a certain target distance of this secondary structure typeLABEL=ab9 ... ALPHARMSDa label for the action so that its output can be referenced in the input to other actionsALPHARMSD...Probe the alpha helical content of a protein structure. More detailsRESIDUES=55-60this command is used to specify the set of residues that could conceivably form part of the secondary structureTYPE=OPTIMALthe manner in which RMSD alignment is performedLESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12}calculate the number of a residue segments that are within a certain target distance of this secondary structure typeLABEL=ab10 ... ALPHARMSDa label for the action so that its output can be referenced in the input to other actionsALPHARMSD...Probe the alpha helical content of a protein structure. More detailsRESIDUES=61-66this command is used to specify the set of residues that could conceivably form part of the secondary structureTYPE=OPTIMALthe manner in which RMSD alignment is performedLESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12}calculate the number of a residue segments that are within a certain target distance of this secondary structure typeLABEL=ab11 ... ALPHARMSDa label for the action so that its output can be referenced in the input to other actions
#radius of gyration Calpha:GROUPDefine 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 detailsNDX_FILE=index.ndxthe name of index file (gromacs syntax)NDX_GROUP=C-alphathe name of the group to be imported (gromacs syntax) - first group found is used by defaultGYRATIONCalculate the radius of gyration, or other properties related to it. More detailsTYPE=RADIUSThe type of calculation relative to the Gyration Tensor you want to performATOMS=Calphathe group of atoms that you are calculating the Gyration Tensor forLABEL=rga label for the action so that its output can be referenced in the input to other actionsNOPBCignore the periodic boundary conditions when calculating distancesPBMETAD...Used to performed Parallel Bias metadynamics. More detailsLABEL=biasa label for the action so that its output can be referenced in the input to other actionsARG=rg,ab1.lessthan,ab2.lessthan,ab3.lessthan,ab4.lessthan,ab5.lessthan,ab6.lessthan,ab7.lessthan,ab8.lessthan,ab9.lessthan,ab10.lessthan,ab11.lessthanthe input for this action is the scalar output from one or more other actionsHEIGHT=0.1the height of the Gaussian hills, one for all biasesPACE=200the frequency for hill addition, one for all biasesBIASFACTOR=20 #ADAPTIVE=DIFF #GRID_WFILES=GRID.0,GRID.1,GRID.2,GRID.3,GRID.4,GRID.5,GRID.6,GRID.7,GRID.8,GRID.9,GRID.10,GRID.11use well tempered metadynamics with this bias factor, one for all biasesGRID_WSTRIDE=2000 #GRID_RFILES=GRID.0,GRID.1,GRID.2,GRID.3,GRID.4,GRID.5,GRID.6,GRID.7,GRID.8,GRID.9,GRID.10,GRID.11frequency for dumping the gridSIGMA=0.2,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1the widths of the Gaussian hillsGRID_MIN=-10,-20,-20,-20,-20,-20,-20,-20,-20,-20,-20,-20the lower bounds for the gridGRID_MAX=50,20,20,20,20,20,20,20,20,20,20,20the upper bounds for the gridUPDATE_FROM=1 ... PBMETADOnly update this action from this time
# metainfSAXS...Calculates SAXS intensity. More detailsLABEL=test2a label for the action so that its output can be referenced in the input to other actionsATOMS=2017-2288The atoms to be included in the calculation, eMARTINICalculate SAXS for a Martini modelNOPBC#ADDEXPVALUES #RESCALE #NUMQ=19 #SCEXP=1680 SCALEINT=1680Ignore the periodic boundary conditions when calculating distancesQVALUE1=0.01100010Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,QVALUE2=0.02127519Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,QVALUE3=0.03155028Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,QVALUE4=0.04182537Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,QVALUE5=0.05210046Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,QVALUE6=0.06237555Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,QVALUE7=0.07265064Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,QVALUE8=0.08292573Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,QVALUE9=0.09320082Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,QVALUE10=0.10347591Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,QVALUE11=0.11375100Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,QVALUE12=0.12402609Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,QVALUE13=0.13430118Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,QVALUE14=0.14457627Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,QVALUE15=0.15485136Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,QVALUE16=0.16512645Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,QVALUE17=0.17540154Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,QVALUE18=0.18567663Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,QVALUE19=0.19595172Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2,EXPINT1=1667.55Add an experimental value for each q valueEXPINT2=1439.16Add an experimental value for each q valueEXPINT3=1157.47Add an experimental value for each q valueEXPINT4=897.121Add an experimental value for each q valueEXPINT5=685.309Add an experimental value for each q valueEXPINT6=524.694Add an experimental value for each q valueEXPINT7=407.433Add an experimental value for each q valueEXPINT8=323.015Add an experimental value for each q valueEXPINT9=261.99Add an experimental value for each q valueEXPINT10=217.205Add an experimental value for each q valueEXPINT11=183.73Add an experimental value for each q valueEXPINT12=158.26Add an experimental value for each q valueEXPINT13=138.495Add an experimental value for each q valueEXPINT14=122.736Add an experimental value for each q valueEXPINT15=109.728Add an experimental value for each q valueEXPINT16=98.6766Add an experimental value for each q valueEXPINT17=89.2737Add an experimental value for each q valueEXPINT18=81.5691Add an experimental value for each q valueEXPINT19=75.5662 ... SAXSAdd an experimental value for each q value
#lsaxs: STATS ARG=(test2\.q_.*) PARARG=(test2\.exp_.*)METAINFERENCE...Calculates the Metainference energy for a set of experimental data. More detailsSCALEDATA#NOISETYPE=MOUTLIERSSet to TRUE if you want to sample a scaling factor common to all values and replicasNOISETYPE=MGAUSSfunctional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)AVERAGING=200 #ARG=(test2\.q_.*),bias.bias REWEIGHT PARARG=(test2\.exp_.*)Stride for calculation of averaged weights and sigma_meanSCALE_PRIOR=FLAT #SCALE0=1.00 SCALE_MIN=0.995 SCALE_MAX=1.005 DSCALE=0.001either FLAT or GAUSSIANSCALE0=1.00initial value of the scaling factorSCALE_MIN=0.5minimum value of the scaling factorSCALE_MAX=2.0maximum value of the scaling factorDSCALE=0.001maximum MC move of the scaling factorSIGMA0=0.1initial value of the uncertainty parameterSIGMA_MIN=0minimum value of the uncertainty parameterSIGMA_MAX=30maximum value of the uncertainty parameterDSIGMA=0.1maximum MC move of the uncertainty parameterADDOFFSETSet to TRUE if you want to sample an offset common to all values and replicasOFFSET_PRIOR=FLAT #OFFSET0=-5 OFFSET_MIN=-6 OFFSET_MAX=4 DOFFSET=0.01either FLAT or GAUSSIANOFFSET0=-9initial value of the offsetOFFSET_MIN=-20minimum value of the offsetOFFSET_MAX=20maximum value of the offsetDOFFSET=0.01maximum MC move of the offsetOPTSIGMAMEAN=SEMSet to NONE/SEM to manually set sigma mean, or to estimate it on the flyLABEL=bqa label for the action so that its output can be referenced in the input to other actionsWRITE_STRIDE=10000write the status to a file every N steps, this can be used for restart/continuationSTRIDE=10 ... METAINFERENCEthe frequency with which the forces due to the bias should be calculated
#ensaxs: ENSEMBLE ARG=(test2\.q_.*),bias.bias REWEIGHT #statsq: STATS ARG=(ensaxs\.test2\.q_.*) PARARG=(test2\.exp_.*)
#bq: RESTRAINT ARG=statsq.corr AT=0 KAPPA=0 SLOPE=-1000000 STRIDE=2FLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More detailsSTRIDE=1000 #PRINT FILE=q.dat ARG=statsq.*,lsaxs.* STRIDE=100 #PRINT ARG=(test2\.q_.*) FILE=CV.dat STRIDE=100 #PRINT FILE=ENSAXS ARG=(ensaxs\.test2\.q_.*) STRIDE=100 #PRINT FILE=RESTRAINTS ARG=bq.* STRIDE=100 #STRIDE=100 FILE=colvar #PRINT ARG=rg,ab1,ab2,ab3,ab4,ab5,ab6,ab7,ab8,ab9,ab10,ab11the frequency with which all the open files should be flushed