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ir:0,Then:[24,63,67,151,152,162],There:[0,3,4,5,6,11,16,23,24,41,59,63,74,76,80,85,87,96,99,114,124,128,129,130,135,138,140,148,149,150,152,153,155,156,159,160,161,163,164],These:[0,2,3,4,6,9,12,16,19,24,28,31,34,61,87,104,106,110,124,125,126,127,128,129,130,131,134,137,138,139,142,144,146,148,149,151,152,153,158,159,160,162,163,164],Use:[0,5,10,11,12,24,26,28,29,32,35,36,39,41,45,46,47,49,53,56,59,64,66,73,86,87,89,93,94,95,97,98,99,100,101,103,104,107,108,109,111,112,114,115,117,118,120,122,124,133,137,149,150,152,159,161],Used:[152,159,161],Useful:[23,41,56,114,150,157,159],Uses:[0,159],Using:[0,2,6,8,9,12,18,20,23,31,80,92,113,114,124,125,133,155,161],With:[0,7,12,21,24,29,30,32,33,34,35,37,53,54,55,56,59,62,64,66,73,74,75,76,77,80,83,87,89,94,96,101,103,104,110,111,114,115,116,117,118,120,123,125,128,129,134,137,138,145,149,151,152,159,161,164],_force_inlin:132,_gmx_:11,_mod:24,_mpi:24,_prev:158,a_0:28,a_1:[28,44],a_2:44,a_3:44,a_idealga:56,a_n:28,aalten:73,abbrevi:[11,148],abi:24,abil:[17,133],abin:66,abl:[1,4,10,16,17,19,24,52,73,130,138,139,141,150,151,158,163],abort:76,about:[0,1,2,3,4,6,10,12,16,24,25,33,34,52,58,63,64,87,103,108,116,122,130,131,133,134,137,141,142,143,144,145,148,150,152,153,155,156,158,159,160,161,162,164],abov:[0,1,3,5,7,9,12,13,16,19,20,21,24,56,67,71,79,104,114,122,124,125,133,152,156,158,159,160,161,162,164],abrt:76,abs:[49,162],absenc:[3,158,162],absent:63,absolut:[6,10,16,24,33,41,48,49,64,71,138,139,141,149,159,161,162],abstol:33,absurd:128,acc:159,accdir:73,acceler:[25,63,131,134,137,140,142,143,148,149,150,156,159],accept:[4,21,24,25,31,73,124,141,148,159],acceptor:[66,87],access:[3,4,11,17,25,48,101,124,130,133,148,156,161,162],accessor:[3,11],accident:[127,145],accommod:[159,160],accomplish:[3,28,160],accord:[0,6,11,20,21,24,25,27,45,67,73,80,87,114,115,120,139,148,151,158,159,161],accordingli:[12,24,61,148,159],account:[16,24,27,31,36,39,40,42,45,61,73,77,81,90,149,151,159,161],accumul:[129,137,158,159],accur:[56,80,108,110,126,159,164],accuraci:[0,24,52,90,101,114,116,150,159],acf:[28,29,34,44,45,49,56,64,66,97,110,118,120],acflen:[28,29,34,45,49,56,64,66,97,110,118],achiev:[0,3,24,53,139,142,148,151,159,161,162],acid:[34,87,108,145,155,162],acpyp:163,acpypi:155,acquir:10,acronym:11,across:[4,24,25,40,41,57,80,87,90,101,111,114,117,148,152,158,159,161,162,164],acs:162,acsig:120,act:[7,24,76,120,137,138,159,161],action:[2,21,24,156],activ:[0,76,116,134,137,146,147,159,161,162],actual:[0,1,2,3,6,8,9,12,16,17,19,21,23,24,28,31,54,62,63,68,116,123,124,126,128,130,136,138,139,145,151,153,158,159,160,161,162,164],acyl:85,adapt:[12,24,73,116,128,139,140,148,156,160],add:[0,1,3,5,6,10,16,19,20,21,24,31,35,42,49,53,61,87,106,114,116,122,123,128,148,149,150,151,156,159,161,162,163],add_definit:0,added:[0,3,6,23,24,27,28,53,57,61,76,87,106,125,126,130,132,133,136,138,139,140,141,148,152,159,162],addendum:153,adding:[3,19,21,24,76,87,116,128,132,133,145,150,162],addit:[0,2,3,5,6,11,16,19,21,23,24,28,30,31,66,76,87,101,104,105,108,111,114,124,125,130,131,134,136,148,151,152,159,161,162,164],addition:[0,3,5,9,21,24,35,40,63,83,87,95,134,143,159,160,161],address:[16,130,146,164],addresssanit:0,addresssanitz:0,addtogroup:3,adeeeeeeeffff:152,adequ:[24,164],adher:[6,17,20,127,139,155,158],adiabat:56,adip:45,adjust:[0,120,133,160,161,164],admin:[6,9,12,20,21],administr:[156,161],adress:159,advanc:[0,10,148],advantag:[5,7,24,95,114,133,135,142,148,152,159,160,161,162],advic:[24,76,156,157,159,162],advis:[63,149,155],aexp:[28,29,34,44,45,49,56,64,66,97,110,118],affect:[3,4,6,7,9,11,16,76,93,128,130,138,146,158,159,161],affin:[76,133,161],afford:127,aforement:24,after:[0,3,5,7,9,12,16,19,25,28,31,35,37,53,63,71,73,76,86,87,96,114,116,124,130,134,138,146,148,150,152,156,158,159,160,162,163,164],afterward:[46,114,134,164],again:[0,12,24,37,53,81,108,125,158,159,160,161,162],against:[0,3,6,16,19,24,41,53,128,149],aggreg:[31,161],aggress:0,ago:94,agre:[10,127],agreement:[10,151],ahx:67,ahxend:67,ahxstart:67,aim:[0,2,12,161,164],aix:24,aka:24,ala:162,alanin:162,alchem:159,algebra:153,algorithm:[1,35,46,49,73,76,88,101,130,137,140,148,149,150,152,157,158,159,160,162,164],alias:[10,57,114],align:[10,53,89,106],aligncent:53,aliphat:155,alkyl:151,all:[1,2,3,4,5,6,7,9,10,11,12,16,17,19,20,21,23,24,27,28,29,30,32,33,34,35,39,45,47,49,51,52,53,55,56,57,59,61,62,63,66,67,71,73,74,76,81,84,85,86,87,89,90,93,94,95,96,98,99,101,103,104,107,108,109,110,112,114,115,116,117,120,122,123,124,125,126,127,129,131,132,133,134,135,136,137,138,139,140,142,145,146,147,148,149,150,151,152,155,156,158,159,160,161,162,163,164],all_forc:111,all_veloc:111,alldih:122,allic:150,alloc:[10,108,126,136,143,152,161],allow:[0,3,6,8,12,18,19,21,23,24,36,40,51,53,56,59,60,63,71,76,86,87,101,114,120,124,126,130,136,137,138,139,148,149,150,152,156,159,160,161,162,163],almost:[11,24,31,74,152,159,161,162,163],alon:[19,24,131,159,162,164],along:[3,27,41,43,52,53,63,64,73,82,85,116,120,124,125,129,130,131,140,149,158,159,160,162],alongsid:[123,133],alpha:[3,25,28,67,68,73,148,159],alphabet:[3,7],alphanumer:[124,130],alreadi:[16,21,24,40,80,106,124,130,134,137,138,145,150,151,161,162],also:[0,2,3,4,6,7,9,10,11,12,16,17,19,20,21,23,24,28,29,30,31,32,34,37,39,40,41,44,45,48,50,52,56,57,59,63,66,68,71,73,74,75,76,77,80,81,83,84,85,87,89,90,94,95,96,101,103,104,105,106,108,110,114,116,118,120,122,123,124,125,126,127,128,129,130,131,132,133,134,136,137,138,139,140,141,142,143,144,146,148,150,151,152,153,155,156,158,159,160,161,162,163],alter:[21,24,76,124,152,161],altern:[3,10,16,21,24,26,71,74,87,93,123,141,148,149,152,159,161,164],although:[4,12,33,55,96,124,139,152,159,161],altivec:24,altloc:124,altogeth:123,alwai:[0,3,5,10,16,24,28,31,34,35,46,56,66,76,86,101,114,120,124,125,127,128,129,131,136,137,138,140,142,148,149,150,151,152,153,159,161,162,164],am1:159,amadei:73,amax:42,amb2gmx:155,amber03:155,amber94:155,amber96:155,amber99:155,amber99sb:155,amber:[87,134,150,157,162,163],amberg:155,ambigu:[3,137],amd64:24,amd:[24,131,132,134,140,150,161],amdappsdkroot:24,amdgpu:161,amend:21,amino:[34,87,108,145,162],aminoacid:122,among:[24,159,161],amongst:113,amount:[3,23,38,46,61,66,108,113,126,134,143,151,160,161,162],ampersand:104,amplifi:84,amplitud:[84,159],amu:[87,94,159],anadock:[25,148],anaeig:[25,39,81,126,148],analog:[94,159,164],analys:[17,26,27,28,29,56,83,103,120,135,164],analysi:[10,12,16,20,24,28,29,34,39,42,46,53,59,64,66,72,73,76,81,103,104,114,124,131,132,133,138,149,152,155,157,159,162,164],analysisdata:[3,19],analyt:[28,134,142,150,159],analyz:[6,9,20,27,32,34,35,39,46,48,55,64,66,81,83,103,104,107,109,112,115,120,136,163],andersen:159,ang:[66,85],angav:[29,59],angdist:29,angew:[35,159],anghist:59,angl:[3,6,7,25,32,34,45,52,53,59,63,65,66,67,68,70,76,78,85,87,89,94,97,104,107,120,121,122,126,131,134,145,148,151,152,159,162],angletyp:151,angstrom2:159,angstrom:[52,159],angular:[42,87,159,164],ani:[0,3,6,7,9,10,12,16,17,19,21,24,28,33,34,35,53,56,58,63,68,71,73,76,77,85,87,96,103,104,106,115,124,125,126,130,132,133,134,137,138,139,142,144,145,148,149,150,152,156,158,159,160,161,162,163,164],anim:[35,119],anis:96,aniso:96,anisotrop:[96,117,159],anneal:150,annot:[2,3,6,20],announc:134,anonym:3,anoth:[3,9,24,35,46,54,59,76,77,103,113,114,124,127,129,130,138,151,159,161,162,164],anotheraccessor:3,ansi:24,answer:[17,23,24,157,158],antechamb:[155,163],antialias:152,anyon:[150,155],anyth:[3,4,19,104,124,128,130,133,145,149,150,152,160,164],anytim:164,anywai:[63,85,130,143],anywher:[11,124],apart:162,api:[4,6,11,12,19,23,128,150,161],appar:130,appear:[3,6,7,23,24,29,73,103,124,130,142,152,161,162,164],append:[0,24,30,55,76,113,116,124,127,148,157,159,160],appl:24,appli:[3,4,5,6,11,20,21,24,25,34,39,53,54,62,68,73,104,108,120,124,125,137,139,150,151,153,155,158,159,161,162,164],applic:[3,21,24,35,87,149,159,161,162,164],approach:[10,12,19,24,26,27,125,159,161,162],appropri:[3,4,10,24,60,76,90,101,104,116,134,146,153,155,156,159,161,162,163,164],approxim:[27,40,55,58,88,101,105,129,152,153,159,161],apu:[24,161],aqueou:164,arbitrari:[41,73,108,136,151,159,162],arch:[134,137],architectur:[0,6,17,24,125,126,128,130,134,140,149,150,158,161],archiv:[9,24],area:[1,10,12,23,25,41,48,51,101,148,159],aren:151,arg:[34,87],arginin:87,argo:101,argu:[155,159],argument:[10,11,19,21,24,34,52,76,81,114,116,124,128,141,143,148,151,160],argv:16,aris:[130,141,162,164],arithmet:[23,128,148,151,157,158,160],arm64:131,arm:24,arm_neon:[24,128],arm_neon_asimd:24,armclang:[24,128],armv7:24,armv8:24,arnold:139,aromat:[34,87],around:[3,10,24,25,41,45,49,53,56,62,66,67,68,70,71,82,84,85,93,106,107,108,109,115,116,120,121,124,131,138,142,143,145,146,148,149,151,156,159,160,161,164],arrai:[19,91,126,128,129,159],arrang:[24,158,163],arriv:150,arrow:52,artefact:162,articif:159,articl:[87,149,153,161],artifact:[9,149,159,162,164],artifici:160,asan:0,asan_symbolizer_path:0,ascend:[124,160],ascii:[28,39,152,153],ask:[23,24,54,66,89,113,115,129,138,156,157,161,162,164],asn:34,asp:[34,87],aspart:87,aspect:[6,8,76,124,138,150,156,161],assembl:[24,162,163],assert:[0,4,10,19,126,129,138],assess:[153,161],assign:[1,10,16,25,34,35,48,65,71,94,100,103,106,120,124,139,145,148],assist:[24,155,162],assoc:10,associ:[3,6,24,66,158,161],assum:[3,6,21,24,28,29,31,34,36,47,48,51,58,59,65,66,71,76,82,84,86,90,93,101,103,112,114,120,122,133,136,138,139,149,150,156,159,160],assumpt:[132,143,153],asymmetr:160,asymmetri:160,asynchron:[150,161],atan2:127,atb:151,atm:[77,159],atom1:152,atom2:152,atom3:152,atom4:152,atom:[0,24,25,27,29,32,33,34,35,36,37,39,40,41,42,45,47,49,50,51,52,53,55,57,58,59,61,62,63,64,65,66,67,68,70,71,73,74,75,76,77,78,80,81,85,86,87,89,91,93,94,95,96,97,100,101,103,106,107,108,109,110,111,112,114,115,116,118,119,122,125,126,128,132,134,136,138,141,149,150,151,152,155,156,159,160,161,163,164],atom_expr:124,atomarea:101,atomist:[149,163],atommass:94,atomnam:[41,148],atomname2typ:122,atomnr:[99,124],atomnumb:138,atomtyp:[63,122,124,159,162],attach:53,attemp:158,attempt:[10,11,24,41,63,71,76,128,129,130,134,138,152,158,159,160,161,162],attent:[6,162],attract:123,attribut:[6,20,21],audienc:19,august:131,author:[3,6,7,58],auto:[0,24,76,116,120,125,126,134,161],autocorr:28,autocorrel:[25,28,34,40,44,45,49,56,66,97,110,118,148],autodock:[25,26,148],autom:[24,139,140,150,151,159,161,163],automat:[0,2,3,5,6,7,8,9,16,20,23,24,31,41,61,81,87,116,117,120,123,124,130,132,137,139,148,149,150,152,159,161,162,163],autoscal:111,avail:[0,1,2,3,4,5,10,13,18,19,24,25,40,44,66,76,116,120,124,125,130,131,133,134,136,138,139,140,142,145,148,149,150,151,152,154,155,156,159,160,161,162,164],availab:161,availbl:24,avclust:36,avek:159,aver:[42,45,56,83,97,148],aver_start:28,averag:[25,26,27,28,29,30,31,32,34,35,39,40,41,42,43,45,46,47,51,55,56,57,59,65,66,67,68,70,73,75,80,82,83,84,89,93,94,95,96,97,100,101,108,109,110,111,120,125,128,130,138,148,150,152,157,159,161],averarea:48,avercorr:29,averdist:148,avgrp:94,avoid:[0,3,4,10,11,12,24,76,85,91,120,133,136,139,141,142,149,151,159,160,161,162,164],avx2:24,avx2_128:24,avx2_256:[24,128,142],avx512:[24,125,131],avx:[24,125,137,149,150],avx_128_fma:[24,128,142],avx_256:[24,128,142],avx_512:[24,128],avx_512_knl:24,awai:[19,39,81,128,130,145],awar:[24,84,128,133,159,161,162],awh1:159,awh:[25,76,140,148,161],awhinit1:159,awhinit2:159,awhinit:[76,159],awkward:24,axes:[25,32,53,64,91,93,104,148],axi:[32,41,42,43,44,45,49,52,53,59,64,65,67,68,85,91,93,98,117,118,123,124,127,129,131,152,159,160],axial:[25,42,148,159],b3lyp:159,b7e4f30d:130,b_i:28,back:[0,9,10,24,76,81,114,122,130,133,150,157,159,160],backbon:[34,67,89,108,152,159,164],background:[24,120,150,155,157,162,164],backslash:156,backup:[25,150],backward:[28,66,135,148,149],bad:[24,41,130,159,162,163,164],bad_alloc:[3,4,10],badli:153,balanc:[76,116,131,133,142,149,150,158,159,161],ball:[119,164],ballenegg:139,bandwidth:24,bank:[26,32,34,46,52,80,85,96,104,111],bar:[25,28,132,148,159,164],barint:31,barker:159,barost:139,barostat:[152,163],barrier:[139,140,159],base:[0,3,5,6,10,11,16,20,21,24,25,26,27,41,45,49,51,53,56,62,65,66,71,72,73,80,86,87,93,102,108,125,126,128,132,134,138,141,142,145,148,149,150,151,158,159,160,161,162],baseclass:3,baselin:[10,24],basevers:0,bash:[20,21,24],bashford:159,basi:[51,152,159],basic:[0,4,5,10,19,20,25,73,103,104,116,124,130,148,164],bat:24,batch:[24,133,150],bath:[106,151,159],bayesian:120,bcpo:116,bdevout:116,bdhdl:116,bdn:116,bear:162,beauti:123,becaus:[2,3,6,10,12,19,24,31,46,52,63,73,89,117,120,124,125,126,128,130,131,134,142,149,150,152,153,158,159,161,162,163,164],becom:[24,62,124,130,137,139,159,161,164],been:[0,1,3,5,6,11,12,16,19,21,23,24,27,42,53,57,71,73,76,119,124,125,130,131,132,133,134,137,138,140,141,143,148,149,151,155,158,159,160,161,162,164],befor:[0,1,2,3,4,10,12,16,19,20,24,28,34,35,53,56,63,71,73,76,79,81,87,96,98,116,120,124,125,126,127,128,130,133,137,145,148,149,150,151,152,155,158,159,160,161,162,163],beforehand:16,begin:[3,11,28,29,31,34,40,44,45,49,56,64,66,81,97,110,118,124,155,159,161,162,164],beginfit:[28,29,34,45,49,56,64,66,80,97,110,118],beginn:164,behav:[4,17,19,24,71,151,161],behavior:[0,10,21,25,124,141,143,145,150,161],behaviour:[17,24,41,73,126,130,132,133,141,151,159,161],behind:[130,159],being:[10,23,24,41,66,103,124,126,127,130,132,133,137,138,143,144,150,151,152,155,160,161,162,163,164],belief:24,believ:24,belleman:[29,78],belong:[3,26,34,162],below:[3,4,5,6,8,10,11,12,17,19,20,21,24,42,59,67,86,95,114,120,124,131,133,134,140,148,149,150,152,159,160,161,162,164],bench:116,benchdev:116,benchdhdl:116,benchedo:116,bencherr:116,benchfld:116,benchmark:[24,116,150],benchn:116,benchpf:116,benchpx:116,benchrnav:116,benchrot:116,benchrota:116,benchrott:116,benchswp:116,benchtpi:116,benchtpid:116,bend:[25,68,148,152],benefici:24,benefit:[10,24,131,134,161],bennett:[25,31,148],beo:116,berendsen:[34,73,130,139,140,141,156,159,162,163,164],berthelot:[134,159],besid:24,best:[3,10,12,17,24,128,133,145,148,151,155,159,160,161,162,164],beta:[3,88,124,159],beta_i:159,beta_new:159,beta_old:159,betafactor:124,better:[1,3,4,10,11,19,21,24,81,114,116,126,127,128,130,131,142,145,149,150,157,158,159,162,164],between:[2,3,6,7,10,16,21,23,24,28,29,30,31,32,33,34,35,36,41,42,45,47,49,51,53,55,56,58,59,60,61,62,65,66,67,71,72,75,76,77,80,83,86,87,88,89,94,95,99,103,104,106,107,108,109,114,115,116,117,118,124,128,131,133,134,137,138,139,140,149,150,151,152,156,157,159,160,161,164],bewar:[24,53,113,159],beween:159,beyond:[3,86,151,158,159,161,162,164],bfac:[37,96],bfact:[34,53],bfg:159,bfield:116,bfit:[40,44],bgclang:24,bham:55,bhamsr:55,bia:[30,139,159],bias:[104,137,140],bibtex:24,big:[3,60,124],bigger:164,bilay:[41,155,160,163],bin:[16,19,24,31,34,41,42,47,48,51,59,93,94,100,104,108,109,111,117,120,156,159],binari:[0,2,8,9,10,11,12,19,21,23,25,35,63,76,87,94,114,128,130,134,138,143,148,150,151,152,153,156,158,159,160],bindex:104,binspac:117,binutil:24,binw:[47,59,148],binwidth:[28,29,34,43,59,66,70,100,107,111,117],bio:[149,161],biochemistri:156,biolog:[25,41,73],biomol:73,biomolecul:[155,164],biomolecular:155,biophi:34,biopolym:156,bisect:[31,43,49],bit:[10,24,41,67,126,133,134,149,158,161,164],bitmask:136,bitwis:[130,142],bla:24,black:[35,152],blank:145,blanket:10,blen:148,blind:162,blindli:162,blink:24,block:[3,5,7,19,28,31,43,54,56,60,62,70,120,124,126,129,134,137,141,148,150,152,159,161],blog:[24,153,161],blow:[17,150,157,162,163],blue:[6,12,123,152],bluegeneq:24,bmax:[34,94],bmin:94,bmtx:116,board:24,bodi:[5,6,161],boltzmann:[31,35,53,56,104,159],bolzmann:104,bond:[23,24,28,33,34,50,52,59,63,66,67,76,81,87,89,94,122,125,131,132,135,144,150,151,152,155,156,157,158,161,163,164],bondedtyp:152,bondi:58,bondtyp:151,bonhi:33,bonlo:33,bool:[3,138],boost:161,bootstrap:120,born:[159,161],borrow:156,boss:155,both:[0,3,4,6,9,10,11,12,16,17,19,24,27,28,31,32,33,41,48,53,56,57,58,59,68,70,71,72,76,77,79,84,85,87,93,101,102,106,110,111,123,124,125,126,129,130,133,134,136,138,143,148,149,150,152,155,159,161,162],bottleneck:[159,161],bottom:[28,32,35,53,152,159,161],bound:[24,62,72,87,126,128,129,152,159,161],boundari:[24,36,39,40,47,51,59,77,80,86,90,93,95,100,101,103,106,108,112,114,117,120,122,124,138,151,157,159,162],boundsonli:120,box:[24,25,33,40,41,42,45,51,53,57,58,60,65,70,71,73,77,85,90,93,106,110,111,114,119,125,128,130,133,138,145,148,150,151,152,154,156,159,163,164],boxcent:[108,114],boxheight:159,boxlength:[65,90],bpf:116,bpx:116,bra:116,brace:[5,9],bracket:[6,7,152,159],branch:[3,4,21,128,130,131],breakdown:[162,164],brick:114,bridg:[24,25,87,148,152],brief:[3,6,9,148,164],briefli:3,bring:130,brk:[27,32,33,34,35,37,39,40,42,47,48,53,57,58,59,60,61,62,63,64,67,71,73,74,75,76,77,79,80,82,84,86,87,91,93,94,95,96,98,101,102,103,106,107,108,110,111,112,114,115,116,117,118,122],bro:116,broad:130,broader:[3,12,139],broke:132,broken:[19,21,50,114,132,136,138,162,164],bronz:24,brook:67,brookhaven:152,brownian:159,brows:[2,3,9],broyden:159,brs:116,brt:116,bruce:153,brunav:116,bsd:24,bsprof:120,bsre:120,bsresult:120,bswap:116,btpi:116,btpid:116,buckingham:[55,105,149,159],buffer:[76,125,126,132,134,149,150,159,161,162],bug:[3,6,10,17,18,20,24,131,134,141,146,148,164],buggi:129,bugzilla:126,build:[4,6,8,10,12,16,18,21,23,60,76,130,133,134,137,139,142,148,150,151,152,155,157,160,161,162,163],build_shared_lib:126,build_test:[0,19],builder:[151,163],buildinfo:0,buildtyp:0,built:[0,2,3,6,10,12,13,14,15,16,19,20,24,63,106,116,132,139,141,148,150,156,161],bulg:159,bulk:[6,43,56,70,133,159],bulldoz:24,bullet:164,bump:133,bun_dist:32,bun_kink:32,bun_kinkl:32,bun_kinkr:32,bun_len:32,bun_tilt:32,bun_tiltl:32,bun_tiltr:32,bun_z:32,bunch:108,bundl:[2,12,24,25,132,148],burn:159,bvit:40,bwn:43,bypass:63,c12:[105,159],c99:[10,24,133,161],c_p:56,c_v:56,cabinet:161,cach:[8,9,23,24,134,150,161],caf:40,calc:159,calcdist:85,calcul:[25,28,29,31,33,34,35,36,37,39,40,41,42,44,45,47,48,49,51,53,55,56,58,59,63,64,65,66,67,68,70,73,76,77,78,80,81,84,85,86,90,91,93,94,95,96,97,100,101,102,103,104,107,108,110,111,112,115,117,118,120,124,131,136,139,140,142,148,149,150,151,153,155,158,162,164],caleman:159,call:[3,4,10,16,19,24,27,48,63,114,116,130,132,138,148,150,152,153,156,158,161,162],callabl:4,caller:[4,128],calpha:[38,62,67,68],camelcas:11,can:[0,2,3,4,5,6,7,9,10,11,12,16,17,19,20,21,23,24,25,27,28,29,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,48,49,50,51,53,55,56,57,59,61,62,63,66,71,73,74,75,76,79,80,81,83,84,85,86,87,88,92,93,94,95,96,97,98,99,100,101,103,104,105,106,107,108,110,111,113,114,115,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,132,133,134,137,138,139,140,141,142,143,145,146,147,148,149,150,151,152,153,155,156,158,159,160,161,163,164],cancel:[128,159],candi:6,candid:6,cannot:[0,2,3,4,16,19,20,24,53,85,87,125,130,138,141,150,152,153,159,162],canon:159,cap:162,capabl:[24,40,132,142,161],capac:[56,81,142,159],capit:[11,31,61],captur:[10,164],carbon:[25,85,94,148],care:[0,9,19,24,40,120,139,143,145,150,151,159,160,161,162,163],carefulli:[39,63,163],carl:159,carlo:[35,88,100,148,159],carri:[76,120,158],carriag:132,cartesian:[76,81,84,108,159,161],cascad:164,caseit:96,caselectron:159,casorbit:159,casscf:159,cast:10,casual:161,cat:113,catastroph:158,categor:152,categori:[0,159,161],caught:[4,136],caus:[1,3,7,11,16,17,19,34,106,126,127,129,130,133,134,137,138,149,159,161,162,163,164],caution:155,caveat:24,caviti:[150,159],cbin:107,cccccc:152,ccmake:24,cdf:120,cdt:18,cell:[42,61,76,114,129,130,138,150,159,161,164],center:[32,35,36,41,42,45,53,59,65,67,68,71,80,93,106,107,108,109,111,114,115,120,121,124,128,138,139,145,148,150,159,160,164],cento:24,centr:164,central:[3,34,35,77,108,155,158],central_limit_theorem:158,cerda:139,certain:[0,3,9,10,16,19,24,40,53,73,76,114,116,117,125,134,148,149,159,161,162],certainli:[24,31],cfg:[20,21],cflag:24,cfnorm:103,cfrac:103,cgi:126,cgnr:152,ch2:152,ch3:130,chain:[27,37,48,53,74,85,87,124,129,136,145,151,159,164],chainsep:87,challeng:164,chanc:24,chandler:[28,29,66],chang:[0,1,3,4,5,6,7,8,9,10,11,12,16,19,21,23,38,41,42,48,54,58,63,73,87,93,106,111,113,114,119,120,124,125,126,127,128,131,132,137,144,146,147,150,156,157,159,160,161,164],changeid:1,channel:[120,150,159],chaotic:[130,158],chapter:[24,81,87,122,124,151,156,162,163],charact:[5,76,121,124,126,127,152],charg:[38,40,41,45,53,61,64,78,87,88,90,99,106,109,122,124,128,138,139,148,149,150,151,152,153,159,161,164],chargegroup:152,chargegrp:87,charmm19:155,charmm22:155,charmm27:155,charmm36:155,charmm:[134,142,151,157,163],chau:[70,85],check:[0,2,3,4,5,6,9,10,11,16,19,20,21,24,25,27,28,35,50,60,63,67,76,77,81,87,94,96,107,114,116,120,122,124,125,139,148,149,150,152,156,158,159,160,164],checkbox:152,checker:[0,2,3,7,8,9,12,20,23],checklist:157,checkout:[13,14,15],checkpoint:[50,63,76,116,127,128,131,137,138,144,152,156,157],checksum:[76,158],chem:[28,31,35,45,66,101,139,155,156,159,160,162,164],chemic:[25,34,87,122,155],chemistri:[76,155],cheng:164,chew:162,chi:[25,28,48,148],chi_1:34,chi_2:34,chi_3:34,chi_4:34,chi_prod:34,child:60,chimera:151,chip:24,chiprodhisto:34,chiproduct:34,choic:[1,21,24,40,87,130,139,140,142,151,158,159,161,163,164],choos:[11,16,24,53,75,87,104,106,116,129,130,137,138,148,151,156,158,159,161,162,163],choosen:0,chose:[129,138],chosen:[24,80,87,89,120,130,133,149,150,151,152,155,158,159,161,162,164],chunk:162,circl:44,circuit:124,circumfer:104,circumst:[130,161,162],claim:145,clamp:130,clang:[0,20,24,128,161],clarifi:[1,132],clariti:[3,11],clash:[161,164],classhelp:10,classic:[81,149],classif:3,clean:[0,1,6,7,21,24,87,130],cleanup:[126,145],clear:[10,11,93,126,128,130,145,152,163],clearer:10,clearest:11,clearli:[11,84,163],clid:35,client:[24,76],clj:72,clock:[24,128,142,150,161],clone:21,close:[3,11,12,19,23,27,28,33,71,106,124,128,130,134,152,153,159,162,164],close_xtc:152,closer:99,closest:[35,93,109,114,115,124,137,159],clust:[35,36,46],cluster:[25,26,36,46,108,114,125,134,142,148,150,151,158,160,161,164],clustercent:127,clustsiz:[25,148],clutter:11,cmake:[2,3,6,8,9,12,13,14,15,16,19,20,21,23,126,130,132,133,139,142],cmake_:24,cmake_build_typ:0,cmake_c_compil:9,cmake_c_flag:[0,24],cmake_c_flags_:0,cmake_cxx_flag:0,cmake_cxx_flags_:0,cmake_include_path:24,cmake_install_prefix:[16,24],cmake_library_path:24,cmake_prefix_path:24,cmake_skip_install_rpath:16,cmakecach:24,cmakein:3,cmakelist:[0,6,12,16,24],cmap:[45,87],cmax:123,cmbi:48,cmdlineprogramcontext:16,cmin:123,cmp:52,coars:[114,163],coarser:161,code:[2,4,6,7,8,9,10,16,17,18,19,23,24,34,123,127,129,131,132,133,136,137,138,139,140,142,145,150,152,156,158,159,161,162],codebas:[8,23],codelet:24,coeff:56,coeffici:[80,159],cog:124,coher:3,coil:152,cold:[162,164],cole:44,coli:73,collect:[0,3,4,8,12,73,113,118,159,161],colon:152,color:[6,34,35,36,45,48,55,115,119,123,150,152],colormap:[123,152],colour:46,colum:161,columb:159,columm:159,column:[28,31,44,71,86,103,104,120,123,125,148,152,159,161,162],com:[3,20,21,51,76,107,109,111,115,124,125,126,130,137,148,161],comb:[152,159,162],combin:[17,24,25,31,41,44,50,54,76,87,92,99,103,105,110,114,123,124,128,130,131,135,139,141,142,148,149,150,151,152,156,159,161,162],come:[3,7,16,17,24,86,133,134,147,152,159,160,161,162,164],comfort:24,comm:[137,159,161],comma:[10,161],command:[0,2,3,9,12,17,19,21,23,32,44,52,54,56,62,76,87,113,114,116,119,122,123,126,132,133,134,139,150,152,156,157,158,160,161,162,163],commandlin:16,commenc:163,comment:[2,3,6,7,10,12,18,23,28,63,71,127,141,152,162],commerci:24,commit:[0,8,17,18,20,23,24,129,130,138],common:[2,5,6,9,10,12,18,20,23,24,25,35,41,119,124,129,130,133,138,151,157,164],commonli:[10,11,24,136],commrec:141,commun:[73,76,127,129,134,137,138,149,150,159,160,161],comp:[27,31,160,164],compact:[3,108,114],compani:156,compar:[6,10,21,25,33,37,41,50,63,66,71,94,127,133,138,142,148,149,152,159,161,164],comparis:130,comparison:[21,50,52,55,94,96,124,139,157,159,161],compart:[133,159],compat:[0,10,24,27,35,36,39,42,43,45,46,48,55,66,70,75,94,95,103,104,117,123,124,125,133,134,135,137,148,149,150,152,155,159,161],compatibl:10,compens:[36,159,162],competit:24,compil:[2,3,4,7,10,11,12,16,17,19,20,33,116,134,138,142,150,151,158,159,160,161],compilervar:24,complain:[3,20,130,143,159],complaint:130,complement:12,complet:[0,2,9,24,28,35,76,79,80,94,120,150,151,152,155,156,158,159],complex:[2,3,10,11,19,24,41,53,76,103,124,126,139,151,160,161,164],compliant:[25,148],complic:[24,41,135,151],compon:[2,12,16,19,27,28,29,30,44,45,47,49,54,56,62,64,72,85,89,91,93,109,111,112,120,128,150,159,160,161,164],compos:124,composit:149,compound:162,comprehend:152,compress:[24,41,56,76,116,148,152,159,164],compressibl:41,compromis:124,comput:[0,3,10,24,25,27,29,31,34,36,37,40,41,42,43,45,46,47,48,49,52,53,54,56,58,59,61,64,65,66,67,70,72,73,74,76,77,79,80,81,85,86,90,92,93,94,95,96,98,100,101,102,108,110,111,115,117,118,119,120,124,126,128,132,134,137,138,139,140,142,143,145,148,149,150,151,152,153,155,156,158,160,162,164],computation:[88,159],compute_glob:138,con:120,conc:61,concaten:[25,54,73,113,114,124,148,152],concentr:[61,159],concept:[0,12,16,124,161,162],concern:[0,18,155,157,159],concert:163,conclus:164,concurr:[150,161],cond:3,condens:155,condit:[0,10,24,36,39,40,47,59,77,86,87,93,95,100,101,103,106,108,112,114,122,124,125,129,148,157,158,159,162],condition:7,conduct:[40,160],cone:124,conect:[53,101,114],conf1:[37,79],conf2:[37,79],conf:[34,53,60,62,63,74,87,122],config:[0,6,7,9,12,16,20,21,24],configur:[0,3,5,9,10,12,16,21,47,58,59,71,73,86,93,101,103,106,112,114,128,130,132,137,141,148,149,150,151,152,158,159,160,162,163,164],configure_fil:0,confirm:[17,143],conflict:[4,124],conform:[1,5,20,21,25,39,60,62,71,76,79,87,98,114,148,156,159,162,164],confout:[76,116],confrm:[25,52,148],confus:[3,85,128,133,136,141,145,159,162],conic:159,coninu:159,conjug:[151,159],conjunct:[150,159,162],connect:[66,76,101,133,145,152,159,161,162],connolli:101,consecut:[62,87,89,121,129,137],consequ:161,conserv:[140,146,157,158,159,161,162],consid:[3,4,5,6,10,16,17,24,35,36,39,58,66,77,81,86,90,93,94,101,107,111,114,120,124,126,151,156,157,158,159,162],consider:[16,18,34,41,128,134,162,163],consist:[1,3,5,6,7,9,10,12,21,23,33,35,47,71,75,89,101,106,107,110,115,118,124,126,130,133,136,145,148,150,152,154,159,161,162,163],consol:[16,19],consolid:11,const_cast:10,constant:[10,11,25,28,34,40,44,45,56,62,63,66,73,80,87,105,110,120,122,124,126,128,148,149,158,159,161,162,164],constf:73,constr:[62,81,159],constrain:[111,126,132,138,159,161,162],constraint:[36,62,63,73,81,131,133,135,149,150,151,152,155,158,159,160,161,163,164],construct:[6,10,11,18,19,20,62,63,74,116,124,130,139,145,156,159,160,162],constructor:[3,10],consult:[24,149,150,155,162,164],consumpt:[0,139],contact:[3,25,33,66,75,77,148,162],contain:[0,1,3,5,6,7,8,9,10,11,12,16,19,21,23,24,28,29,31,34,36,40,41,44,45,46,52,55,56,59,62,63,66,68,71,73,76,85,86,87,91,93,95,103,104,108,111,113,116,118,120,121,123,124,126,128,129,130,136,138,146,147,148,149,150,152,155,156,158,159,161,162,163],content:[0,2,3,5,9,12,23,24,27,33,62,63,76,152,156,158,162],context:[5,11,12,28,126,158],contibrut:159,contigu:114,contin:159,continu:[3,4,10,16,20,24,40,61,63,68,76,87,103,114,116,124,125,128,133,137,150,151,152,157,159,161,162,163],contour:34,contract:73,contrari:162,contrast:[3,124,130,156],contrib:12,contribut:[16,23,86,125,129,134,137,138,149,150,153,159,162],control:[0,2,4,11,19,20,21,24,31,40,55,73,79,87,94,103,116,120,124,130,139,148,151,152,157,162],conv:35,conveni:[0,3,5,10,12,20,21,24,59,63,128,130,160,161],convent:[8,12,18,23,87,124,157,161,162],converg:[40,58,139,158,159],convers:10,convert:[2,10,42,48,53,54,63,84,87,94,96,105,114,123,124,126,149,151,152,155,158,159,160,162],convolut:[133,159],convolv:159,coo:87,cool:150,cooper:[3,158],coord1:159,coord:[108,111,112,159],coordin:[30,33,40,41,42,52,53,57,60,63,67,68,73,74,76,79,80,81,87,90,96,103,106,108,110,111,112,114,115,117,120,122,124,125,126,127,130,131,132,137,139,142,145,151,152,158,159,160,161,163,164],coordsel:120,cope:[159,164],copi:[6,10,12,16,21,24,63,71,87,108,114,125,127,137,141,145,150,151,152,156,158,159,161,163],copyright:[3,5,9,20,25],copyrightmod:21,core:[10,24,34,76,119,130,140,142,149,157,158,159,160,161,164],core_rotam:34,corner:[24,53,130],cornerston:158,corr:[34,45,56],correct:[0,1,3,5,6,10,16,19,21,31,33,36,39,40,53,54,56,62,63,73,81,87,90,104,111,117,123,130,135,136,146,150,151,155,159,160,161,162,163,164],correctli:[2,3,4,6,24,54,72,128,129,130,133,138,139,140,149,159,164],correl:[25,28,29,31,34,40,45,49,56,64,66,96,97,110,117,118,139,148],corresond:96,correspond:[3,7,12,19,27,32,40,41,46,55,58,59,64,66,68,73,79,84,87,96,103,113,120,122,123,128,146,147,148,149,150,152,159,160,161,162,164],correspondingli:[11,139],corrupt:[24,76,150],cos:[28,29,34,45,57,89,107,159],cosav:45,coscont:28,cosh:110,cosin:[27,28,29,34,45,65,89,104,107,110,159],cost:[10,39,93,98,100,128,130,133,134,139,159,161,162,164],coul14:55,coul:[55,72,159],could:[3,4,10,16,24,35,112,114,125,130,132,134,136,138,143,145,149,151,156,158,160,161,162],couldn:162,coulom:159,coulomb:[55,72,76,116,129,133,138,149,150,159,161],coulombtyp:[138,152,155,159],coulr:55,coulsr:55,count:[29,35,42,48,73,75,77,108,125,130,136,138,142,150,159,161],counter:[0,116,125,161,162,163],coupl:[34,41,51,63,73,116,117,126,127,130,131,142,151,156,158,160,161,164],cour:24,cours:[33,79,108,120,130,159,164],coval:81,covar:[25,27,29,73,128,148],covara:39,covari:[24,28,39,73,128],cover:[6,19,23,24,49,74,76,84,103,120,139,155,156,159,161],coverag:[0,20,100,141],cpack:[0,16,20],cpi:[63,76,116,133,158],cpnum:[76,116],cpo:[76,116,158],cpp:[3,11,16,19,21,126,133,156],cppcheck:[0,12,20],cppcheck_xml_output:0,cpptraj:130,cpt:[27,29,32,33,34,35,36,39,40,41,42,43,45,46,47,48,49,50,51,57,58,59,60,63,64,65,66,67,68,70,73,75,76,77,79,80,81,82,84,85,86,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,107,108,109,110,111,112,113,114,115,116,117,118,119,133,150,156,158],cpu:[24,76,131,139,140,142,146,149,150,152,159,161,162],cpuinfo:142,cpuinfotest:126,cqq:72,crai:161,cramer:159,crash:[4,17,19,29,73,76,114,128,129,130,138,159,162,163,164],crazi:[162,164],creat:[0,3,6,8,9,18,19,23,24,38,50,79,96,106,108,116,120,124,126,127,145,148,150,151,152,160,161,164],crew:122,crippen:94,critera:159,criteria:159,criterion:[45,87,124,164],critic:[16,24,58,159],cromer:102,cross:[2,12,24,68,97,130],crosscompil:24,crosslink:23,crude:53,cryptic:[16,126],cryst1:152,crystal:155,csize:36,csizew:36,cstdio:7,ct400626b:[139,162],ctest:[0,11,19,20],cth:152,ctime:111,ctrl:[76,138,158],cube:[53,108,164],cubic:[53,58,110,114,159,164],cuda:[0,10,125,131,138,142,150,161],cuda_host_compil:24,cuda_path:24,cuda_visible_devic:139,cudalaunchkernel:150,cue:152,cufft:24,cumbersom:126,cumlt:103,cumul:[28,34,93,103,109,120,162],current:[0,1,2,3,4,5,6,7,8,10,11,12,16,18,21,23,24,25,50,51,76,87,100,103,110,112,120,122,124,130,136,137,139,142,148,150,152,156,159,160,161,162,163,164],curs:24,curv:[24,28,93,100,117],custom:[0,2,3,5,10,12,16,19,20,24,50,124,150,159,164],customiz:16,cut:[23,24,35,36,53,63,66,76,93,99,114,128,129,133,134,138,139,152,156,157,159,161,164],cutoff:[26,33,35,62,66,86,115,116,124,128,145,148,149,150,152,155,159,160,161,162,164],cxx:24,cxxflag:24,cxxx:150,cyan:152,cycl:[6,10,73,116,120,125,142,150,154,161],cyclic:[6,12,120,156],cyl0:159,cyl1:159,cylind:159,cylindr:159,cyn:155,cystein:155,cyx:155,d2v:159,daccddddddee:152,dai:[24,136,145,149,161],damp:141,dan:66,danger:87,dangl:137,danum:66,dark:6,dash:[148,152,159],dat:[16,34,39,41,42,43,48,51,53,55,68,71,76,87,91,94,95,100,102,103,106,120,121,124,127,151,160,163],data:[0,1,3,4,8,10,12,19,23,24,25,26,28,30,31,32,34,39,41,42,43,44,46,48,51,52,53,54,55,56,68,76,80,83,85,87,91,94,95,96,100,102,103,104,111,113,118,120,121,122,123,132,133,135,137,141,145,148,150,152,158,159,160,161,162,163],databank:152,databas:[16,34,53,71,87,106,122,152],dataset:73,date:[0,3,6,24,120,130,146,150,155,161],daura:35,david:[153,159],dawson:153,dbool:137,dbuild_shared_lib:24,dcmake_build_typ:[0,24],dcmake_c_compil:24,dcmake_cxx_compil:24,dcmake_cxx_flag:24,dcmake_cxx_link_flag:24,dcmake_install_prefix:24,dcmake_prefix_path:24,dcmake_toolchain_fil:24,dcuda_toolkit_root_dir:24,ddcheck:[76,161],ddorder:[76,161],dds:[76,161],deadlock:130,deal:[24,124,162],debat:155,debian:24,debug:[0,1,10,19,24,63,66,67,68,94,126,128,157,158],debugg:[17,19],deby:[44,45,100],decai:[110,139,159],decent:[24,159],decid:[3,4,17,133,151,159,164],decim:[31,114,125,150,152,153,159],deciph:11,decis:[4,162,163],declar:[0,3,6,10,11,12,19,116,152],decompos:[150,161],decomposit:[76,125,128,133,134,136,137,138,139,141,144,150,152,157,159,164],decompositon:159,deconvolut:137,decoupl:[133,159],decreas:[53,125,159,161],decrstoreu:130,dedic:[108,161],deduc:[1,31,94],deep:10,deepli:5,defbutton:152,deffnm:[76,116,128,158,160],defgroup:[3,6],defin:[0,3,4,6,7,10,12,29,32,33,35,42,45,46,48,51,59,60,63,64,66,68,70,71,73,76,82,87,89,97,107,109,119,120,122,124,125,127,130,132,133,139,148,150,151,152,156,161,162,163,164],definit:[0,3,6,10,23,24,66,78,87,130,132,151,159,161,162,163],deform:[84,159],defun:5,deg:159,degrad:161,degre:[29,31,34,36,45,53,59,66,67,81,82,84,87,104,111,121,124,128,159,164],delai:161,delet:[10,24,74,116,162],deliber:[0,128,138,164],delimit:[5,24,152],delin:58,delta:[31,56,138,159],delta_f0:73,delta_t:129,deltaf0:73,deltaf:73,deltalambda:31,demand:[20,24,65,88],demo:156,demonstr:[3,19],demux:[113,138],den:41,denomin:[10,24],denorm:143,denot:12,denschlag:164,densiti:[25,40,42,43,49,53,71,93,101,106,117,138,148,152,159,161,163],density4d:43,densmap:[25,148],densord:[25,148],dep:[0,6],depart:162,depend:[0,2,3,7,10,12,16,19,20,24,25,31,35,40,44,45,56,58,71,73,96,104,106,110,114,116,124,125,126,128,134,148,149,150,151,152,155,158,159,161,162,164],depgraph:6,depict:35,deploi:161,deploy:[2,24],deprec:[24,128,135,137,149,150,159],depth:152,der:[33,34,53,58,60,71,106,120,150,164],deriv:[3,28,31,44,56,66,104,116,129,137,138,159,163,164],descend:11,descent:[132,159],descib:159,describ:[0,3,6,8,9,10,12,19,20,24,35,41,73,103,124,133,137,141,145,149,150,151,152,158,159,160,162,163,164],descript:[0,3,4,6,9,10,11,17,19,24,127,130,148,152,156,162],deshuffl:33,design:[0,3,9,10,19,24,158,159,162,164],desir:[0,1,16,24,56,73,83,87,111,124,141,159,162,164],desk:161,desktop:[24,161],despit:159,desrib:9,destabil:73,destructor:3,det:30,detail:[2,3,4,5,7,9,12,19,20,21,23,24,25,31,35,41,66,70,74,76,81,85,103,110,116,124,131,133,140,146,147,149,150,151,154,157,159,160,161,162,164],detect:[0,2,6,24,108,114,126,132,139,143,145,150,158,161],deterior:[125,159,161],determin:[0,3,6,24,31,35,40,45,46,52,53,58,65,66,67,76,77,80,85,87,88,89,98,109,110,114,116,117,120,124,130,139,151,152,158,159,160,161,164],determinist:158,deuter:[85,87],deuterium:85,dev:[0,3,12,137,161],develop:[0,2,3,5,9,10,16,18,19,24,141,146,148,150,155,158,161],developer_zon:23,deviat:[10,11,28,31,35,37,39,47,58,67,83,94,95,96,101,120,138,143,153,159],deviati:[76,116],devic:[0,24,76,116,130,132,137,150,161],device_nam:150,devout:[76,116],dflexibl:159,dft:159,dgmx_binary_suffix:24,dgmx_blas_us:24,dgmx_build_mdrun_o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rawn:152,dregressiontest_download:24,drift:[56,149,159,161],driftcorr:56,drive:[73,159],driver:[24,138,148,161],drmax:46,drnum:46,drop:[24,114,159],dropov:114,dropund:114,drsum:46,dsp:40,dssp:[48,150],dtermin:52,dual:140,due:[1,4,5,27,33,41,58,63,76,117,124,125,134,136,138,145,158,159,161,162,164],dull:123,dummi:[3,66,91],dump:[25,29,48,63,66,94,114,119,130,148,150,152,158],duplic:[74,120,124,127,129,151],dure:[0,16,21,23,24,31,45,63,71,73,77,81,87,113,114,116,124,128,138,143,146,150,151,152,157,158,159,161,163],dvar:137,dvariable1:63,dvariable2:63,dye:[25,51,148],dyecoupl:[25,148],dymdom:52,dyn:73,dyn_:124,dyn_mol_cog:[47,58,59,71,86,93,101,103,112],dyn_mol_com:[47,58,59,71,86,93,101,103,112],dyn_res_cog:[47,58,59,71,86,93,101,103,112],dyn_res_com:[47,58,59,71,86,93,101,103,112,124],dynam:[0,16,23,24,28,51,73,76,86,103,112,114,116,124,126,140,148,150,152,155,157,158,160,161,162],dynamic_cast:10,dyndom:[25,148],e_0:55,e_a:56,e_b:56,e_fre:55,each:[0,1,3,6,7,8,9,10,12,19,20,21,24,26,28,31,32,34,35,39,41,42,47,48,50,54,55,58,59,60,63,64,65,66,68,71,73,76,77,80,82,83,85,86,89,91,93,94,95,96,99,100,101,103,104,107,109,110,111,112,113,114,115,116,120,121,124,126,133,134,145,148,149,150,152,156,158,159,160,161,162,163,164],earli:[10,143,164],earlier:[4,5,24,41,48,128,137,141,156,162],easi:[7,10,11,16,17,19,21,39,80,142,152],easier:[19,20,24,50,124,149,156,160],easiest:[6,41,156],easili:[2,3,5,17,19,93,101,148],ecacccccddddd:152,eccacccccdddd:152,echo:138,eclips:18,edccabcccdddd:152,edccbabcccccd:152,edcccbabccccc:152,edccccbabcccc:152,eddccccbacccc:152,edg:[6,24,101,152],edi:[73,76,116,128],edist:104,edit:[24,25,38,62,148,156,159,162,163],editconf:[25,71,106,148,156,163],editor:[5,74,152,156,163],edittext:152,edock:26,edr:[30,31,33,45,50,54,55,56,63,72,76,83,116,127,130,150,158,159],edsam:[76,116],effect:[0,6,41,53,56,61,73,104,114,128,130,131,142,148,149,150,157,159,161,162,164],effici:[24,48,51,73,76,133,139,142,149,159,160,161],effort:[0,6,16,128],efit:[40,44],efl:73,efl_nul:73,eflnul:73,efre:26,eig2:[27,126],eig:[27,35,73,126],eigcomp:27,eigenfreq:81,eigenv:[27,39,73,81,82],eigenval2:27,eigenvalu:[27,39,73,81,82,83,84,89,128,133,159],eigenvec2:27,eigenvec:[27,39,73,81,82,84],eigenvector:[25,27,35,39,56,73,76,81,82,83,84,89,128,136,148],eight:161,eigio:126,eignr:84,eigrmsf:27,eigvec:73,einstein:[40,80],eint:44,eisenhab:101,either:[0,3,6,10,24,26,31,59,61,66,71,76,86,87,103,111,114,124,130,131,137,142,148,149,151,152,155,156,158,159,160,161,162,164],eiwit:[26,85,87,96],ekr:111,ekrot:111,ekt:111,ektran:111,elaps:[150,158,159,160,161],elec:161,electron:[41,145,159],electrophysiolog:[74,150],electrostat:[53,88,90,149,161,164],element:[3,6,10,35,39,61,81,85,100,123,128,136,139,152,159],elig:116,elimin:[35,87,158,159,160],elj:72,ellipt:67,els:[3,7,10,12,19,24,63,123,133,152,159,161,162,163],elsewher:[151,160,161],emac:[18,156],email:[3,24],emat:55,emax:104,emb:[76,143,160],embed:[2,6,24,76,130,132,157,159],emerg:0,emin:104,emphas:159,emphasi:17,empir:159,emploi:162,empti:[0,3,6,7,21,71,91,130,150,159,163],emstep:159,emtol:159,emul:150,enabl:[0,2,24,40,87,116,124,125,126,130,132,134,138,139,140,148,149,150,159,161,162],enabled_sect:3,encad:159,encapsul:[121,123,152],enchanc:127,enclos:[3,124],encod:[151,153],encompass:162,encount:[16,24,108,150,152,156],encourag:[24,149],end:[3,5,7,10,11,16,24,28,29,31,34,38,40,44,45,49,56,64,66,80,81,83,89,97,100,102,110,113,118,119,124,125,126,127,134,142,146,150,152,158,159,160,161,164],endcond:3,endfit:[28,29,34,45,49,56,64,66,80,97,110,118],endif:[63,152,156,162],endintern:3,endmdl:152,endpoint:[59,148],endq:[100,102],ene:104,eneconv:[25,148,150,152],enecorr:56,enemat:[25,148],ener2:33,ener:[30,31,33,45,50,54,55,56,63,72,76,83,104,116,159],energet:[25,148],energi:[26,30,31,33,38,41,45,50,52,54,55,63,66,72,73,76,83,84,101,102,104,111,116,120,128,130,132,139,140,142,144,149,150,151,154,155,157,158,160,161,163],energygrp:[72,159,160],energygrp_excl:160,enerpr:[152,159],enforc:[5,7,8,9,12,21,161],engin:[24,76,139,151,153,159],enhanc:[24,73,116,131,134,161],enlarg:116,enough:[3,10,11,12,16,24,61,108,110,130,141,150,153,159,160,161,162,164],enqueu:161,ensembl:[25,31,35,56,63,73,81,82,83,104,125,128,138,139,140,148,150,160,163,164],ensur:[0,2,3,16,20,24,57,76,93,101,106,108,114,120,125,133,138,149,150,159,161,162,164],ent:[27,32,33,34,35,37,39,40,42,47,48,53,57,58,59,60,61,62,63,64,67,71,73,74,75,76,77,79,80,82,84,86,87,91,93,94,95,96,98,101,102,103,106,107,108,110,111,112,114,115,116,117,118,122],enter:[87,124,152,156,159,160,164],enthalpi:[56,81,104],entir:[24,36,41,84,87,108,137,161,164],entiti:[3,7,12],entri:[53,87,114,116,122,129,136,138,141,150,151,152,159],entropi:[27,31,56,104],enumer:[3,11,148],env:137,envelop:160,enviro:24,environ:[0,16,19,21,23,24,48,87,116,120,125,128,139,157,159,161,162],environment:24,epel:24,eps0:[44,159],eps:[27,28,29,30,31,34,35,36,37,40,41,42,43,44,45,46,48,49,51,53,55,56,57,64,65,67,70,72,77,79,80,83,85,89,90,91,92,94,95,96,97,98,104,105,107,108,109,110,111,114,117,118,121,123,150],epsilon0:44,epsilon:[25,40,44,45,105,148,149,150,159],epsilon_r:90,epsilonrf:45,epsrf:44,epsw:44,eqq:72,eqstep:73,equal:[5,21,24,27,29,34,46,49,53,57,63,64,88,116,124,127,137,138,150,153,158,159],equat:[25,34,43,51,72,150,158,159,164],equibilibr:106,equidist:28,equil:159,equilibr:[116,120,133,138,141,145,151,159,160,162,163,164],equilibrium:[122,158,164],equipartit:[84,164],equiv:95,equival:[0,85,95,148,150,158,161],equlibr:106,eref:55,ergod:159,err:116,errbar:28,errest:28,erron:[126,128,137],error:[1,3,8,16,17,18,19,23,24,25,28,31,54,56,63,76,80,88,96,124,129,133,137,141,143,148,150,151,152,157,158,159,161,164],errorbar:28,escap:3,escobedo:159,esham:104,esp:[27,34,37,39,53,60,61,62,63,67,71,73,74,76,79,87,106,116,122],especi:[24,66,73,109,125,138,141,159,161,162,164],essdyn:76,essenti:[9,24,25,50,73,76,114,148,150,152,161],essl:24,establish:[5,7,164],estim:[25,26,27,28,31,33,38,56,66,72,76,80,88,101,110,118,120,134,148,150,158,159,161],eta:110,eta_0:110,etc:[3,4,6,12,17,18,19,24,47,63,72,73,76,78,87,114,120,124,129,131,138,150,151,152,155,156,159,160,161,162,164],etot:[55,56],euler:[68,159],europort:152,evalu:[0,10,148,151,159,160,163],even:[3,4,5,6,10,11,12,19,24,41,48,76,85,89,93,104,119,124,128,130,131,134,135,138,142,145,149,150,158,159,160,161,162,164],evenli:[109,161],event:[108,158,162],eventu:[63,125,149,158,162,163],ever:160,everi:[0,4,11,12,19,20,21,23,24,27,31,34,35,46,57,62,67,74,87,89,94,98,99,114,120,123,133,139,150,152,153,159,160,161,162,164],everyth:[2,3,10,12,24,25,108,139,148,162,164],everywher:[3,24,130],evid:[3,159],evisco:56,eviscoi:56,evit:40,evolv:[10,12],ewald:[6,40,116,139,142,150,161,162],ewald_beta:88,exact:[3,9,56,83,124,130,145,149,153,157,159,162],exactli:[5,9,35,66,81,95,96,106,114,116,124,126,128,151,153,156,158,160,161,162],examin:24,exampl:[0,1,6,11,17,18,19,20,21,24,45,64,97,98,101,114,116,120,133,134,148,150,151,154,155,159,162,163,164],exce:[76,149],exceed:161,excel:[24,142],except:[0,3,4,5,11,12,16,18,19,28,34,76,120,129,137,138,145,148,149,151,152,159,161,162],excess:[10,159],exchang:[76,134,159],excit:159,excl:[93,159],exclud:[0,3,58,93,145,152,159,160],exclus:[62,80,93,122,125,135,149,150,152,161],exec:114,execut:[0,2,4,9,10,12,16,19,24,48,114,130,142,143,150,156,158,160,161],exercis:152,exhaust:[24,73,153],exhibit:41,exist:[0,1,5,6,8,11,19,24,25,61,66,71,76,87,116,130,133,148,150,159,164],exit:[39,120,141,150,161],exlud:3,exot:151,exp5:[28,29,34,44,45,49,56,64,66,97,110,118],exp7:[28,29,34,44,45,49,56,64,66,97,110,118],exp9:[28,29,34,44,45,49,56,64,66,97,110,118],exp:[28,29,34,44,45,49,55,56,64,66,97,110,118,159],exp_exp:[28,29,34,44,45,49,56,64,66,97,110,118],expand:[3,24,41,63,128],expans:[56,73,159],expect:[3,5,17,24,28,31,55,73,104,116,124,127,128,129,131,133,134,138,139,140,148,149,150,153,158,159,160,161,162,164],expel:73,expens:159,experi:[3,24,41,83,133,159,161,162,164],experienc:[3,161,164],experiment:[24,76,83,96,104],expert:[150,162],expfit:97,expir:158,explain:[1,3,12,16,17,124,125,126,133,151,160],explan:[1,2,6,8,10,12,161,162],explanatori:[133,162],explic:[129,138],explicit:[2,3,10,132,135,137,145,148,155,159],explicitli:[0,3,6,24,27,31,64,79,124,133,150,152,159,161],explod:[133,145,162],explor:73,exponenti:[28,29,34,44,45,49,56,64,66,97,110,118,120,124,153,159],expos:[0,3,11,19,101],expr:124,express:[4,148,153,159,164],ext:20,extend:[4,25,38,63,66,73,122,128,130,132,133,148,151,152,157,159,161],extens:[10,11,19,24,76,114,138,142,148,152,156,159,161,163],extent:[17,54,155],extern:[5,6,7,8,11,12,16,19,23,24,73,103,124,132,139,151,152,158,159,160,161,162],extp:31,extr:27,extra:[3,9,16,19,32,47,58,59,60,71,73,81,86,93,101,103,112,116,133,150,151,152,159,161],extract:[0,2,3,6,9,23,25,30,40,51,55,56,83,101,114,118,148,159,160,164],extrapol:[25,31,52,79,148],extrem:[27,116,140,149,159,164],eye:6,f77:24,f_index:148,fac:159,face:[12,70,164],facilit:[16,155],fact:[114,152,159,162,164],faction:160,factor:[24,28,34,35,37,45,53,54,62,64,71,72,80,87,93,96,102,105,106,111,115,116,122,130,131,134,152,158,159,160,161],fade:148,fail:[0,4,9,10,16,17,19,24,125,126,127,128,130,132,137,150,158,162,164],failur:[4,9,19,129,150,158,164],fairli:[161,162,164],fall:[0,24,133,159],fallback:[16,24],fals:[6,66,108,152],famili:[24,158],familiar:[12,124,156,163],fanci:[19,164],faq:[23,157],far:[125,133,134,159],farther:124,fashion:[161,164],fast:[3,39,87,142,149,150,152,158,159,161,162],faster:[0,24,86,130,131,134,149,150,159,160,161],fastest:[24,116,153,158,161],fat:[24,152],fatal:[4,16,24,63,76,124,126,132,136,137,138,139,141,150,159,161],fault:[17,39,108,137],favor:[25,148],favourit:[5,163],fcstep:159,fcx:156,fcy:156,fcz:156,fddddccccabbc:152,feasibl:[4,10],featur:[0,3,8,16,18,20,23,24,25,53,119,128,140,142,146,148,156,157,161],februari:[126,129],fed:162,fedddccccbabc:152,fedddccccbbab:152,feddddcccccba:152,fee:56,feed:120,feedback:140,fep:[142,159,161],fermi:[24,143,150,161],fetemp:56,few:[0,3,5,6,7,8,9,11,12,16,19,21,24,29,49,128,134,137,139,141,145,148,149,150,158,159,161,164],fewer:[0,134,140,148,161],ffamber:[155,162],ffffff:152,fflush:132,ffn:44,fft:[24,76,97,100,158,159,161],fftpack:[0,24],fftw:[12,132,158,161],ffv:58,fget_lin:132,fglrx:161,fgroup:[47,58,59,86,93,101,103,112,124],field:[23,27,40,44,45,53,61,71,76,80,87,90,106,115,116,122,127,134,138,141,142,145,148,149,150,152,157,161,163],figur:[3,12,17],file:[0,2,4,5,7,8,9,10,12,17,18,19,20,21,23,24,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,126,132,134,139,144,149,150,151,155,157,159,160,161,164],fileand:96,fileio:152,filenam:[63,76,99,116,152,160],fileprovid:96,filesystem:158,fill:[53,71,103,130,158,163],filt:27,filter:[6,20,24,25,27,28,43,114,119,148],find:[0,2,3,7,8,11,12,17,20,23,25,33,50,67,73,137,147,148,150,151,153,155,156,157,159,162,164],fine:[0,24,41,94,126,133,159,161],finish:[125,126],finit:[76,147,158,159,164],first:[0,3,4,6,7,10,11,12,16,17,19,24,26,27,28,29,30,31,32,34,35,36,37,39,40,41,42,43,44,45,46,47,48,49,51,52,53,54,55,56,57,58,59,62,63,64,65,66,67,68,70,72,73,75,76,77,79,80,81,82,83,84,85,86,87,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,123,124,130,132,136,145,148,150,151,152,153,156,158,159,160,161,162,164],firstangl:52,firstmajor:152,fit1:37,fit2:37,fit:[3,24,25,27,28,29,34,35,37,39,40,43,44,45,49,56,57,64,66,67,68,73,79,80,94,95,96,97,98,101,106,108,110,114,118,120,127,128,138,148,159,160,164],fitend:[28,66],fitfn:[28,29,34,45,49,56,64,66,97,110,118],fitgrp:159,fitlog:28,fitstart:[28,66],fitxi:98,five:161,fix:[1,3,4,6,10,17,18,21,41,44,47,54,62,73,86,87,99,113,114,116,124,131,134,141,146,147,148,150,151,152,159,161,162,163,164],fixtur:[11,19],flag:[24,27,28,33,34,40,45,46,63,76,79,87,88,94,96,114,130,148,150,151,156,158,161,162],flat:[24,159],flatten:159,flavor:[18,20,24,128,150],flavour:[125,128],flaw:164,fletcher:159,flex2:159,flex:159,flexibl:[49,81,124,144,149,152,159,163],float_min:128,flood:[73,76],flop:150,flowchart:157,fluc:56,fluct_prop:56,fluctat:159,fluctuat:[25,27,28,40,41,42,43,45,56,57,58,87,96,148,159,161],fluidic:49,flush:143,fly:162,fma:[24,143],fno:0,focu:[3,5,8,19],focus:[0,24,161],foerster:51,foil:[40,133],fold:[9,34,40,108,159],folder:[12,16,24],follow:[0,1,2,3,5,6,7,8,9,10,11,12,17,19,20,21,24,25,28,53,54,56,63,67,72,76,103,104,114,119,120,124,148,149,150,152,155,156,158,159,161,162,163,164],font:[119,123,150,152],fontnam:119,fontsiz:152,foo:[1,11,91],foo_:11,fool:24,footprint:24,forc:[21,23,24,25,35,53,61,62,71,73,76,87,88,106,111,112,114,120,122,124,125,126,129,130,132,135,137,138,141,142,145,148,149,150,152,156,157,158,159,160,161,163],forcefield:[87,122,152,155,163],forcerec_t:137,foreign:[31,159],foreign_lambda:31,forese:135,forget:3,forgiv:162,fork:150,form:[1,4,10,20,35,36,41,42,44,73,79,87,108,124,153,155,159],formal:[130,159],formaldehyd:162,format:[0,2,3,6,8,9,17,18,23,24,26,27,28,29,30,31,32,34,35,36,39,40,41,44,45,46,47,48,49,50,51,53,54,55,56,58,59,63,64,65,66,68,72,73,75,76,77,79,80,81,82,83,84,85,86,87,89,90,91,92,93,94,95,96,97,98,100,101,102,103,104,105,107,108,109,110,111,112,113,114,115,116,117,118,119,120,122,123,124,126,148,150,151,155,156,157,159,162],former:[6,10,24,103,137],formerli:[132,152,159],formula:[3,27,28,100,139],forth:159,forthcom:142,fortran:24,fortun:128,forward:[10,12,28,66,133,156],found:[0,2,4,6,9,16,17,19,20,22,24,52,53,71,73,76,106,117,120,122,134,139,146,147,148,149,151,155,156,159,160,161],foundatom:11,four:[5,59,68,76,120,124,137,141,159,161],fourier:[49,116,118,158,159],fourierspac:159,fourth:[28,159,161],fract:33,fraction:[29,33,40,47,48,58,62,76,88,103,116,144,148,159,160],fragment:12,frame:[0,4,25,27,28,29,30,32,34,35,36,39,40,41,42,43,44,45,46,47,48,49,51,54,55,56,57,58,59,63,64,65,66,67,68,70,72,75,77,80,81,83,84,85,86,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,107,108,109,110,111,112,113,114,115,117,118,119,123,124,126,127,128,137,148,150,152,158,159,160,164],framenr:114,framework:[0,20,24,116,131,148,161],fran:152,free:[2,3,16,24,25,26,30,31,33,36,38,40,54,55,56,58,63,72,73,76,101,104,108,120,129,133,137,138,139,140,148,149,152,160,161,163,164],freedom:[36,81,82,84,111,128,159,164],freeli:159,freeman:156,freevolum:25,freez:[62,150,151,156,159],freezedim:[159,160],freezegrp:[159,160],frequenc:[25,28,44,49,57,63,73,76,81,114,133,139,148,150,159,161],frequent:[23,24,87,157,158,163,164],freshli:3,fret:51,fric:[30,159],friction:[30,137,139,159],friction_tensor:30,friendli:[73,119,152],frog:[142,159,164],from:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,70,71,72,73,74,75,76,77,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,122,123,125,126,129,130,131,132,133,134,136,137,141,142,148,149,150,151,152,155,156,157,158,159,160,162,163,164],front:[3,8,12,24,105,142],frozen:[151,159,160,163],fsanit:0,ftn:24,ftp:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164],fudg:73,fudgelj:[152,162],fudgeqq:[152,162],fulfil:40,full:[0,3,10,21,23,24,25,27,39,47,49,56,63,73,76,80,81,82,84,98,101,108,110,111,114,116,118,130,139,143,145,148,152,158,159,162],fulli:[0,10,16,24,38,41,87,120,125,126,128,131,133,134,148,160,162],fun:[29,150],funct:[73,152,156],fundament:[41,162],further:[0,12,16,19,24,25,45,51,53,63,73,93,128,130,131,139,156,157,158,159,161,162,163],furthermor:[40,45,52,130,156],fuse:24,futur:[0,1,125,130,131,135,143,148,150,156,161],g53a5:122,g96:[27,29,32,33,34,35,36,37,39,40,41,42,43,45,46,47,48,50,51,52,53,57,58,59,60,61,62,63,64,65,66,67,68,70,71,73,74,75,76,77,79,80,82,84,85,86,87,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,106,107,108,109,110,111,112,113,114,115,116,117,118,119,122,151],g_idealga:56,g_lie:72,g_memb:[76,128,160],g_order:148,g_rm:152,g_tool:128,gaff:155,gain:[148,150,161],gamma:159,gangl:[25,124],gap:[24,120],garbag:137,gas:[36,56],gather:[128,161],gauch:29,gauss0:159,gauss:120,gaussian98:108,gaussian:[28,43,73,81,82,120,138,150,159],gbsa:159,gcc:[0,24,127,128,130,132,143,161],gcn:[24,161],gcom:[76,161],gcovr:9,gear:161,gem:28,gemfit:66,gen:[0,73,152,158,159,162],gen_vel:63,genbox:127,genconf:[25,163],gener:[0,4,5,6,7,8,9,11,12,16,18,19,20,21,23,24,27,34,35,39,41,42,43,44,48,51,52,53,55,58,60,61,62,63,68,70,71,73,74,75,76,77,79,81,82,84,85,87,88,94,95,100,101,102,106,108,114,116,120,121,122,123,124,128,130,131,134,136,137,139,142,149,150,151,152,155,156,157,158,160,161,162,163,164],genion:[25,148,164],genrestr:[25,148,151,162],gentler:163,geometr:[53,87,114,134,156,159,160],geometri:[43,120,124,125,130,131,159,164],gerrit:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164],get:[0,1,2,3,4,9,11,12,16,20,21,23,27,31,38,40,48,58,61,63,80,81,101,104,108,111,116,124,125,126,127,130,132,133,136,137,138,139,145,149,150,152,154,157,158,159,162,163,164],ghostview:150,ghz:149,gibb:[66,104,159],gibbs3:104,gibbsdelta:159,gimp:152,git:[0,2,5,6,8,17,18,20,23,24],gitattribut:[20,21],github:21,gitignor:0,give:[17,21,24,27,31,34,44,53,56,63,70,71,73,76,77,85,98,104,110,114,116,117,124,125,130,133,134,136,138,141,152,158,159,161,162,164],given:[0,3,6,12,21,24,25,27,28,31,33,34,35,36,40,44,45,46,51,52,53,56,57,58,60,61,62,70,71,76,77,80,81,85,86,97,99,102,104,110,111,113,114,116,120,124,128,134,148,149,151,152,158,159,160,161,164],gkr:45,gkratom2:45,gkratom:45,glanc:7,glass:[155,164],gln:[34,87],glob:160,global:[3,4,11,73,76,86,128,134,138,150,159,161],globular:160,glu:[34,87],glutam:87,glutamin:87,gly:152,glycin:48,gmax:104,gmock:[7,19,132],gmx:[0,2,3,9,10,12,16,19,24,124,132,141,143,149,150,152,154,155,156,158,159,160,161,162,163,164],gmx_:[11,24],gmx_add_unit_test:19,gmx_allow_cpt_mismatch:150,gmx_assert:[4,10],gmx_binary_suffix:24,gmx_blas_us:24,gmx_bonded_nthread_uniform:150,gmx_broken_calloc:0,gmx_build_for_coverag:0,gmx_build_help:[0,2],gmx_build_manu:[0,2],gmx_build_mdrun_onli:[0,2,12],gmx_build_own_fftw:[0,127],gmx_build_shared_ex:0,gmx_build_tarbal:0,gmx_build_unittest:[0,19],gmx_clang_cuda:[0,24,143],gmx_compact_doxygen:[0,3],gmx_compeldump:150,gmx_compiler_warn:0,gmx_constraintvir:150,gmx_cuda_clang_flag:0,gmx_cuda_nb_ana_ewald:150,gmx_cuda_nb_ewald_twincut:150,gmx_cuda_nb_single_compilation_unit:132,gmx_cuda_nb_tab_ewald:150,gmx_cuda_target_comput:[24,143],gmx_cuda_target_sm:24,gmx_cycle_al:150,gmx_cycle_barri:150,gmx_cycle_subcount:0,gmx_cyclecount:130,gmx_d:116,gmx_data_install_dir:[0,16,24],gmx_dd_debug:150,gmx_dd_npuls:150,gmx_dd_nst_dump:150,gmx_dd_nst_dump_grid:150,gmx_dd_order_zyx:150,gmx_dd_record_load:150,gmx_dd_use_sendrecv2:150,gmx_default_suffix:24,gmx_detailed_perf_stat:150,gmx_developer_build:[0,12],gmx_dipole_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:161,hyperlin:159,hyperthread:161,hyphen:141,hypothesi:163,hypothet:58,iact:120,ianalysisdatamodul:19,ibm:[24,161],ibm_qpx:[24,128],ibm_vmx:24,ibm_vsx:24,icc:[24,128,143,161],icd:24,ice:101,icommandlinemodul:11,id_and_t:87,id_or_t:87,idea:[1,3,11,24,106,124,162,164],ideal:[0,3,10,16,56,67,150],ident:[27,31,35,37,39,66,76,113,114,120,123,130,138,141,152,158,159,160],identifi:[3,6,11,19,21,27,53,71,87,124,130,136,138,145,146,147,163],ifdef:[0,10,63,156,162],ifndef:[3,63],ign:108,ignh:[87,152,162],ignor:[3,6,9,21,24,28,55,71,78,87,106,125,129,149,152,159,161,162,164],igpu:150,iiact:120,ildn:155,ilist:125,illeg:124,illustr:156,imag:[42,51,53,77,94,137,159,162],imagemagick:[2,24],imagin:164,imaginari:[44,159],imbal:[116,150,161],imd:[63,76],imdforc:76,imdgroup:63,imdport:76,imdpul:76,imdterm:76,imdwait:76,imho:130,immedi:[3,11,103,128],impact:[10,124,137,159,161],impl:11,implement:[0,2,3,4,6,8,11,12,16,18,19,20,23,24,73,119,120,126,127,131,133,138,139,148,149,150,151,155,157,158,159,160,161,164],impli:[53,80,93,108,111,113,116,130,159],implicit:[10,149,164],importantli:[139,162],impos:73,imposs:[10,11,16,164],improp:[29,78,87,122,152,164],improv:[1,10,11,24,90,131,135,140,146,148,150],inaccur:[53,114,161],inaccuraci:40,inact:133,inadvert:[3,137],inappropri:[24,132,133,162,164],incid:10,includ:[0,2,3,4,5,8,9,10,11,12,16,18,19,20,21,23,24,34,41,44,45,47,50,51,56,62,63,66,78,80,81,87,95,103,124,125,128,132,133,134,138,139,140,142,148,151,152,155,158,159,160,161,162,163,164],includesort:[6,20,21],inclus:[0,152,159],incom:102,incompat:[87,137,150,162],incomplet:[0,6,73,122,126,162],incomprehens:130,inconsist:[4,128],inconveni:[0,141],incorpor:[125,126,127,128,129,137,141,146,155],incorrect:[2,4,6,16,125,126,135,136,137,141,143,150,159],incorrectli:[24,125,132,133,162],increas:[10,24,39,71,73,76,87,100,104,108,124,126,130,134,139,141,149,150,151,158,159,161],increasingli:24,increment:[35,68,73,134,159],incrementor:159,incrstoreu:130,incur:161,inde:33,indent:[5,9,10,18,20],independ:[28,31,47,86,94,103,110,120,128,149,159,161],index:[2,3,12,19,21,23,25,27,29,30,32,33,35,36,37,38,39,40,41,42,43,45,46,47,48,49,50,51,52,53,57,58,59,61,62,63,64,65,66,67,68,70,71,73,74,75,76,77,78,79,80,82,85,86,87,89,90,91,93,94,95,96,97,98,100,101,102,103,104,107,108,109,110,111,112,113,114,115,116,117,118,119,124,125,126,128,129,133,136,148,150,152,159,161,164],indic:[3,13,17,24,28,29,34,45,49,54,56,62,64,66,73,76,87,88,97,103,104,110,113,118,120,124,126,145,150,153,156,159,160,161,162,164],indirectli:[10,159],indistinguish:126,indivdu:161,individu:[3,12,19,20,24,25,29,31,47,48,59,80,89,99,120,124,134,136,137,145,148,151,158,161],ineffici:[10,159,161],inertia:[25,64,91,148],inexpens:124,inexperienc:164,inf:160,infeas:151,infer:[31,87,113,129,138,149,152],inferior:135,infin:[40,44,45,73,159],infinit:[76,110,149,158,159,164],influenc:[0,3,19,130,150,159,161,163],info:[0,9,25,52,63,67,150],inform:[2,3,5,6,8,9,10,12,13,16,17,19,20,23,24,25,28,31,33,34,35,63,66,87,106,108,114,116,118,122,124,126,128,130,133,136,145,148,150,151,152,155,156,157,158,162,163,164],infrar:159,infrastructur:130,infrequ:[139,159],ingroup:[3,6],inher:[24,139,159,164],inherit:10,inhibit:159,inhomogen:[161,162,164],init:[151,158,159],init_forcerec:130,init_lambda:31,init_step:133,initi:[9,16,19,24,71,73,76,80,106,108,110,114,121,125,126,130,131,137,145,150,152,159,160,161,163,164],initio:159,inlibraryapi:3,inlin:[3,5,10,18,128],innamespac:5,inner:[27,45,104,109,139,140,142],innermost:3,inpr:27,inprod:27,inpublicapi:3,input:[0,3,4,16,17,19,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,128,138,141,145,148,149,150,153,155,158,159,160,164],inputrec:159,ins:150,insensit:150,insert:[0,3,5,25,58,61,66,76,123,127,138,150,151,160,162,163,164],insertcod:124,inserti:71,insid:[3,12,24,25,68,148,151,159,160],insolidangl:148,inspect:[3,6,16,19,35,52,94,161],instabl:[4,17,129,161,164],instal:[0,2,3,6,9,12,16,23,132,133,141,148,150,155,156,157,161,162,163],install_nam:143,instanc:[0,10,24,32,36,42,48,58,87,94,98,150,152,158,160,161],instantan:[46,51,56,83,109,128,138,159,164],instead:[0,3,4,7,10,11,12,16,19,20,21,24,27,30,32,34,35,39,41,42,47,49,50,51,53,55,61,62,63,64,65,71,76,77,83,86,87,93,97,98,110,111,115,116,118,122,124,128,130,133,134,136,137,138,141,142,145,148,150,151,152,153,159,160,161,164],insteff:51,instruct:[0,2,8,20,23,142,150,151,158,161,162],instrument:9,insuffici:[1,137,138,162],int_max:136,intact:[138,164],intdist:89,integ:[124,128,130,136,145,150,151,152,153,159,160,162],integr:[19,20,24,28,40,44,76,90,93,117,120,128,130,139,140,149,152,158,159,160,163,164],intel64:24,intel:[16,140,142,143,149,150,161],intellig:[76,87,161],intend:[0,3,120,126,133,137,138,149,150,151,155,162],intens:100,intent:[3,10,138,141],intention:136,inter:[87,134,150,159,161],interact:[1,9,12,20,24,38,45,50,54,55,56,62,63,72,76,83,87,88,99,113,122,124,128,130,131,132,134,135,138,139,140,144,145,149,150,151,152,156,159,160,163,164],interaction_const_t:137,interaction_funct:129,interest:[0,2,3,16,72,86,93,100,140,148,159,161,163],interfac:[6,10,11,24,43,70,98,106,157],interfaci:43,interfer:161,interleav:[76,161],interm:79,intermedi:[6,35,79,150,159],intermodul:3,intermolecular:156,intern:[0,2,3,4,6,7,11,12,19,20,21,23,24,89,125,126,141,142,159,160,164],internal_doc:3,internet:[17,24],interpol:[25,27,52,79,89,148,150,159],interpret:[3,9,16,28,31,63,73,111,124,156,159,161,164],interrupt:158,intersect:159,interspac:60,interstiti:151,interv:[28,31,57,62,73,76,80,103,114,118,129,138,150,158,159,164],intf:70,intfspect:[43,70],intial:128,intl:159,intra:[12,93,134,148,150,159],intramol:159,intramolecular:164,introduc:[3,11,24,48,127,135,138,141,143,145,146,148,157,159,161,162,163,164],introduct:[0,3,12,19,23,164],introductori:124,intuit:[21,103,124],invalid:[4,6,16,76,133,150],invari:[20,21,142,159],invers:[46,159],invert:[73,104],investig:[17,76,155,160,162],invoc:[21,24,160,164],invok:[0,2,24,48,97,148,150],involv:[39,63,66,73,81,126,155,159,161,163],invsqrt:127,ion:[25,61,99,109,125,133,148,151,152,156,159,162,163,164],ionic:[133,159],ioniz:87,iontyp:159,iontype0:159,iostream:10,iprogramcontext:16,iron:151,irregular:93,irregularli:24,irrelev:63,irrespect:159,irrit:4,isa:150,isn:[136,162,164],iso:159,isol:[19,164],isosurfac:108,isotherm:56,isotrop:[62,117,159],isotropi:159,issu:[0,1,2,3,4,5,8,9,10,18,20,21,23,24,87,120,125,133,134,135,136,138,139,141,142,143,145,146,147,150,153,158,159,160,161,162,164],item:[1,2,3,152,164],iter:[0,1,35,71,114,120,124,150,159,160,161],itp:[62,87,151,156,159],its:[0,2,3,4,6,20,24,27,33,35,41,63,72,76,77,80,85,124,132,142,150,151,152,153,155,156,158,159,160,161,162,164],itself:[3,8,17,19,24,45,56,76,139,156,162,164],januari:140,jarvi:35,javadoc:3,javadoc_autobrief:3,jcoupl:34,jcp:159,jctc:120,jenkin:[0,2,3,4,6,8,12,19,20,21,23,24],jit:130,job:[0,2,3,6,20,24,150,158,161],john:[63,159],join:4,jone:[55,72,76,105,138,149,159,161],jorgensen:155,jot:156,judici:[70,164],jump:[40,57,111,114,117,138,159,164],just:[3,4,9,10,21,24,63,76,87,88,114,116,122,124,131,137,141,143,148,149,150,151,152,153,156,159,160,161,162,164],justifi:[10,11,79,164],k34:110,k40:134,k80:134,kabsch:156,kappa:51,karplu:34,kcal:[120,159],keep:[0,4,5,10,11,19,73,76,101,106,113,114,116,125,128,132,138,146,151,158,159,161,164],keeplast:113,kelvin:82,kepler:161,kept:[3,16,24,63,73,76],kernel:[10,21,24,126,130,131,133,139,143,149,150,161],kessler:156,kev:102,keyword:[63,126,132,148,150,159],khist:51,kind:[0,3,12,24,67,87,134,137,149,151,152,158,159,161,162,163],kinet:[28,66,111,130,138,159,161,164],kink:32,kirkwood:45,kit:24,klein:159,knight:24,knl:[24,125,131,142,143],know:[3,6,10,19,24,25,81,86,126,133,134,148,151,152,153,159,161],knowledg:[6,122,159],known:[8,11,23,24,44,120,124,125,126,127,128,129,132,135,137,139,152,153,155,159],kofk:31,kolev:137,kth:24,kumar:104,l510:150,lab:155,label:[37,53,83,119,123,127,148,152],laboratori:151,lack:[24,128,129,137,138,158],lag:130,lai:6,laid:2,lam:24,lam_a:31,lam_b:31,lambda0:159,lambda1:159,lambda:[10,31,133,159,160],lambda_a:31,lambda_b:31,land:[24,164],landau:159,landscap:104,languag:[3,8,18,23,150,161],lapack:24,laptop:161,larg:[0,3,10,17,36,41,43,46,73,75,76,100,108,114,116,125,126,129,134,139,150,151,153,159,160,161,162,164],larger:[7,53,58,61,67,76,100,106,120,126,134,138,149,151,159,160,161,164],largest:[24,35,36,53,93,124,159,160],laser:159,last:[9,10,27,28,29,30,31,32,33,34,35,36,39,40,41,42,43,44,45,46,47,48,49,51,52,53,54,55,56,57,58,59,63,64,65,66,67,68,70,72,75,76,77,79,80,81,82,83,85,86,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,107,108,109,110,111,112,113,114,115,116,117,118,119,120,124,125,128,129,150,152,158,159,161],lastangl:52,lasten:33,latenc:[24,150,161],latent:[6,137],later:[6,7,10,24,32,45,54,62,76,80,106,113,129,130,134,138,143,149,151,158,159,160,161,162,164],latest:[24,155,161],latex:[0,2,3,9,12,33,152],latter:[3,6,7,16,19,24,44,59,93,124,141,146,161],lattic:60,launch:[116,126,161],law:153,layer:[74,106,131,133,159,160,161,164],layout:[3,6,10],ld_library_path:16,lead:[6,10,11,24,41,73,84,114,124,125,126,128,129,130,132,137,138,141,143,145,151,158,159,160,161,162,164],leaflet:160,leak:128,leaksanit:0,leap:[142,159,164],least:[0,2,8,10,24,35,37,39,51,56,60,73,76,79,80,94,96,98,103,124,126,127,132,133,145,151,159,161,164],leav:[4,42,50,66,106,114,151,159,161,164],led:[126,127,130,132,138],left:[3,35,90,123,124,125,128,130,131,152,164],leftmost:124,legaci:[10,19],legend2label:152,legend:[6,31,53,123,124,152],legendfont:[123,152],legendfonts:152,legendlabel:152,legendr:[28,29,34,45,49,56,64,66,97,110,118],legoffset:123,len:[28,47,67,111,112],length:[5,28,29,32,33,34,44,45,49,53,56,57,64,66,67,77,85,89,97,110,111,112,117,118,149,157,158,159,164],lengthen:159,lengthi:10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0,132,134,135,139,141,143,144,149,150,151,152,156,157,160,161,162,163,164],optionsunittest:11,ora:83,oracl:24,oradiu:68,orang:152,orbit:159,orca:[144,150],order:[2,3,7,9,10,18,20,21,24,25,28,29,34,35,39,43,45,49,54,56,64,65,66,70,73,75,76,79,80,83,97,103,108,110,113,114,115,118,120,124,125,128,130,133,138,148,150,152,156,158,159,160,161,164],ordinari:[114,159],org:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164],org_gmx:24,organ:[0,3,8,10,19,23,142,160],orgir:50,ori:73,orideva:83,oridevr:83,oridevt:83,orient:[24,25,45,53,56,65,71,83,96,98,107,148,159,160,161],orienta:83,orienti:159,orientt:83,origin:[10,16,19,28,31,38,41,67,73,87,114,118,126,127,128,137,145,148,149,151,152,155,158,159,160,164],orinst:[56,83],orir:159,oris:68,oriten:83,orot:68,ort:83,orthogon:[27,64,68,81,84,130],oscil:[25,28,84,148,159,162,164],osmot:120,oten:[56,83],other:[0,1,2,3,5,6,7,9,10,11,12,16,17,18,19,20,21,22,23,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,128,130,132,133,135,136,137,139,141,143,145,146,148,150,151,155,158,159,160,161,162,163,164],otherflag:24,otherlib:159,otherwis:[0,3,6,7,10,20,24,27,28,31,53,63,76,94,101,114,120,124,125,126,128,137,142,143,150,152,158,159,161,162],otilt:68,otl:32,otr:32,otwist:68,ouput:159,our:[0,6,10,12,19,24,41,125,130,132,139,142],ourselv:130,out:[0,2,3,4,6,10,11,12,16,24,33,36,39,41,42,43,47,50,53,54,55,60,61,63,66,68,70,71,73,76,77,79,81,86,87,88,92,103,106,112,114,116,120,122,123,126,128,133,136,138,139,150,156,157,158,159,163,164],outcom:17,outdat:[19,21,23,129,137,141,161],outer:[108,139,140],outfrq:73,outlin:[1,33,161],output:[0,2,3,4,5,6,16,19,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,120,121,122,123,124,126,128,132,133,136,145,148,152,153,156,157,160,161],outsid:[0,2,3,6,9,10,11,19,24,33,139,160,164],outweigh:[134,161],ovec:[56,83],over:[0,1,3,4,12,24,27,28,31,34,42,43,45,47,56,66,75,76,80,83,84,86,88,95,97,100,101,107,108,110,111,125,126,128,130,134,138,139,150,151,152,158,159,160,161,162,164],overal:[0,3,6,19,24,58,62,134,140],overcom:[24,139,140],overestim:159,overflow:[126,128],overhead:[125,129,137,150],overlap:[31,52,60,66,71,108,113,120,137,139,148,150,159,160,161],overload:[10,137],overrid:[61,63,76,112,123,126,150,152,159,160,164],overridden:[21,123,124,130,150,159],overshoot:164,oversight:[129,138],oversubscript:[129,138],overview:[2,3,8,9,20,21,23,156,161],overwhelm:23,overwrit:[88,113,116,121,145,150,151],overwritten:[76,132],ow1:152,own:[0,5,10,17,20,24,27,85,120,124,150,151,152,155,159,160,164],oxt:111,oxygen:[65,124,152,156],oxyz:[47,148],p3m:[150,159],packag:[0,2,3,6,9,12,16,20,24,53,130,132,155,159,163,164],package_sourc:[0,9],pad:128,page:[0,2,6,8,9,16,17,18,19,20,21,23,24,25,147,148,151,155,161,162,163,164],pai:[10,162],pair:[25,33,35,39,45,47,51,55,56,59,62,66,75,76,77,83,86,89,93,95,97,99,122,125,128,138,148,149,150,151,152,158,159,160,161,162],pairdist:[25,47,77],pairwis:[25,47,86,148,159],palmer:110,paper:[31,33,141,153],paragraph:3,parallel:[0,73,76,93,116,129,131,151,158,159,160,161,162,164],parallelepip:164,parallez:125,param1:3,param2:3,param:[3,50,122],paramet:[3,5,10,11,23,25,28,31,34,44,50,53,63,65,70,73,85,88,94,97,100,116,122,123,124,125,126,130,133,134,137,139,140,148,150,151,155,157,158,160,161,163,164],parameter:[157,162,164],parametr:[151,161,164],paremet:150,parent:[16,76],parenthes:[124,159],parrinello:[63,139,140,152,159,162],pars:[0,4,6,31,125,150,159,161,162],part:[0,1,2,3,4,6,8,9,10,11,12,16,17,19,20,23,24,31,32,40,41,44,58,64,67,76,88,110,114,116,124,126,128,130,134,136,142,145,148,151,152,153,158,159,160,161,162,164],part_:124,part_mol_cog:[47,58,59,71,86,93,101,103,112],part_mol_com:[47,58,59,71,86,93,101,103,112],part_res_cog:[47,58,59,71,86,93,101,103,112],part_res_com:[47,58,59,71,86,93,101,103,112,124],parti:[7,17,24],partial:[10,16,23,41,128,136,148,153],particip:161,particl:[25,36,58,66,76,88,93,104,117,136,138,149,150,158,161,163,164],particular:[0,3,5,6,10,11,12,19,20,21,23,24,113,124,126,132,137,142,149,150,158,161,162,163,164],particularli:[0,2,73,76,134,142,161,162,164],partit:[93,159,162],partli:12,partner:138,partxxxx:158,pascal:[134,152],pass:[2,8,10,19,23,24,57,63,76,96,114,116,124,126,130,134,137,145,159,161],past:[24,113,141,143,156],patch:[1,9,20,21,126,128,131,132,137,140,145,147,161],path:[0,6,7,10,12,16,18,19,21,24,79,87,125,128,132,133,142,150],pathscal:24,pathwai:52,patrick:35,patter:21,pattern:[12,21,124,151,156,159],paus:76,paxis1:91,paxis2:91,paxis3:91,pbc:[35,36,37,39,47,51,53,59,73,77,86,93,94,95,100,101,103,107,108,111,112,114,122,124,137,148,150,151,152,159,164],pbcatom:159,pbcdist:51,pcoupl:[152,159],pcoupltyp:159,pdb2gmx:[16,25,122,138,148,151,152,156,157,161,163,164],pdb:[26,27,28,29,30,31,32,33,34,35,36,37,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,55,56,57,58,59,60,61,62,63,64,65,66,67,68,70,71,72,73,74,75,76,77,79,80,82,83,84,85,86,87,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,122,123,124,126,128,138,145,150,151],pdbatom:103,pdbatomnam:148,pdbinfo:136,pdbname:148,pdbq:122,pdf:[0,2,9,12,23,141],pdflatex:24,pdo:120,peak:[81,93,159],penalti:[4,151],peopl:[1,5,16,24,133,139,141],pep:137,peptid:[34,67,73,151,152,156,162],per:[25,27,30,31,34,35,45,46,48,53,55,56,58,65,66,67,73,76,77,85,90,101,107,108,120,125,130,133,135,142,145,148,149,150,159,160,161],percent:[134,161],percentag:[127,150],perf:116,perfect:[6,67,134],perform:[0,3,4,10,21,23,25,27,28,41,53,56,57,73,76,98,116,124,125,127,128,129,131,133,135,137,138,139,140,143,145,146,148,151,152,157,158,159,160,163,164],performac:161,perhap:[24,156,159,162,164],period:[3,12,27,28,29,34,36,39,47,51,53,57,59,76,77,80,84,86,90,93,95,100,101,103,106,108,112,114,117,119,120,122,124,130,149,157,158,159,161,162],perl:[24,155],permiss:[24,128,161],permit:[0,10,24,126,128,130,131,132,134,137,140,149,150,159,161],permitt:159,permolecul:85,permut:[126,130,148],perpendicular:[80,110,159],persist:[89,151],person:[3,7],perspect:161,pertain:[24,162],perturb:[73,125,129,138,149,161],pforc:76,pgi:[24,161],phase:[0,24,31,36,43,70,84,120,137,150,155,159,161],phe:87,phenomena:163,phenomenon:153,phenylalanin:87,phi0:152,phi:[29,34,45,67,92,161],phipsi:67,phosphoserin:155,phosphothreonin:155,phosphotyrosin:155,photorealist:84,phrase:156,phy:[28,31,45,66,70,85,110,139,149,159,164],physic:[76,133,140,151,155,159,160,161,162,163,164],physrevlett:139,pick:[24,125,150],picosecond:[114,159,164],pictur:[3,108,123],piec:[3,151,152,160,162],piecewis:[159,160],piledriv:24,pin:[24,76,125,130,133,137,161],pinoffset:[76,161],pinstrid:[76,161],pipe:[24,124],pipermail:24,pitch:[25,148],pitfal:3,pivot0:159,pivot:159,pixmap:[27,35,36,39,42,43,45,46,48,55,66,70,75,94,95,104,117,123],pkg:[16,24],pkgconfig:24,place:[1,3,6,9,11,12,16,23,41,71,106,114,124,125,126,127,128,129,130,137,138,151,152,153,158,159,160,162,163,164],placehold:12,placement:151,plai:[10,60],plain:[0,19,24,49,81,114,131,134,149,150,159,163],plan:[10,24,129,135,163],planar:[25,34,42,148],plane:[42,53,59,64,80,87,93,97,98,107,110,129,148,159,160],planetari:150,platform:[0,7,10,16,20,23,126,132,133,143,150,152,161],plausibl:161,pleas:[3,5,10,17,23,24,25,36,63,73,81,96,101,103,116,122,131,140,148,149,151,152,155,156,161,162],pleasant:164,plot:[24,25,26,27,28,29,30,31,32,34,35,36,39,40,41,44,45,46,47,48,49,51,55,56,58,59,64,65,66,67,68,72,73,75,76,77,79,80,81,82,83,85,86,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,107,109,110,111,112,113,114,115,116,117,118,119,120,121,123,145,148,152],plu:[19,25,45,53,99,127,130,131,148,152,159,161],plug:150,pm3:159,pmax:104,pme:[6,11,24,25,76,116,130,134,140,148,149,150,152,155,158,159],pme_error:[25,148,151],pmefft:76,pmf:[30,120,137,159],pmin:104,pmx:151,pname:61,png:6,po42:155,po4h:155,point:[3,7,10,13,14,15,17,19,23,24,28,30,31,32,40,44,48,53,55,56,60,73,76,77,80,83,89,104,106,113,118,120,124,125,126,128,129,130,137,138,148,150,151,152,155,157,158,159,160,161,162,164],pointer:[0,10,19,126,130],poisson:53,polar:[25,109,148,155,159],polariz:[76,109,151],polici:11,poll:150,polyatom:133,polym:[25,89,148,155],polynomi:[28,29,34,45,49,56,64,66,97,110,118],polypeptid:87,polystat:[25,148],polyvec:89,pool:35,poor:[0,162],poorli:159,pore:[101,159],port:[10,24,76,130,135,155],portabl:[18,29,30,33,36,38,41,43,45,46,49,50,56,61,63,65,66,67,68,70,76,78,81,83,85,88,89,90,92,97,99,100,109,114,116,119,131,146,152],portion:6,pos_expr:124,pose:17,posexpr:124,posit:[6,25,41,42,47,50,58,59,61,62,63,65,71,73,76,80,82,86,87,88,93,96,101,103,107,108,109,112,117,120,123,133,139,148,150,151,152,156,158,159,160,161,162,163,164],position_restraint:[62,156],positionr:152,posr:[62,87,156,159,162],posre_a:162,posre_b:162,posrefc:87,posres_wat:156,posscript:152,possibl:[0,1,3,4,6,10,11,16,17,19,21,24,35,40,44,63,71,90,98,103,108,114,116,120,124,128,129,132,133,134,136,137,138,144,145,148,150,152,153,158,159,160,161,162,164],post:[1,3,24,148,153],postiv:159,postma:156,postprocess:148,postscript:[25,42,48,75,94,119,121,123,148,152],postyp:124,pot:[120,162],potenti:[7,25,35,53,56,73,76,105,120,126,128,132,134,139,148,149,150,151,155,159,161,162,164],potfit:159,potj:105,pow:105,power6:24,power7:24,power8:[24,125,130,131,161],power:[24,25,28,45,46,49,105,118,136,139,148,158,159,161],powerpc:[24,133],pp_pme:[76,161],ppa:24,pqr:53,practial:159,practic:[10,11,24,76,106,125,128,130,157,158,159,162,164],pre:[20,24,63,71,76,106,128,138,150,162],prec:[31,152],preced:[66,124,127,148,152,161],precentag:161,precis:[0,24,27,31,39,49,56,63,73,76,81,82,83,84,110,111,114,116,118,130,132,139,145,149,151,152,158,159,161,164],precomput:142,precondit:[24,126],predat:3,predefin:[71,151,159],predetermin:5,predict:[150,162,164],prefer:[0,1,3,4,7,10,11,24,120,126,152,161,164],prefetch:[134,150],prefix:[0,3,11,16,24,87,124,150,155,162],preliminari:[1,23,108],prepar:[16,17,18,23,35,127,136,148,157,164],preparatori:108,prepend:[114,124],preprocess:[10,50,132,157,158],preprocessor:[11,18,63,132,152,156,159],prerequisit:[0,23,53],prescrib:20,presenc:[9,33,161],present:[1,4,7,11,20,24,27,28,31,33,36,53,56,71,76,96,103,111,113,120,122,124,133,134,145,148,152,156,159,161,162,164],preserv:[7,57,63,76,87],preset:84,press:[5,24,76,124],pressur:[33,41,76,117,126,127,130,132,133,134,139,142,152,156,157,161],presum:[125,164],pretti:[24,108,161],prev:94,prevent:[12,17,21,24,71,126,130,138,141,143,150,151,156,159,160,162],previou:[1,24,45,62,76,94,116,120,128,133,134,138,148,150,151,156,158,159,160,161,162,164],previous:[1,6,24,76,114,130,133,138,139,162],prframe:100,primari:[24,162],primarili:[2,25,160],prime:159,primer:19,primit:[25,122,148],princ:53,princip:[25,27,28,29,53,64,89,148],principl:[10,56,158,164],print:[0,4,6,16,19,21,25,26,28,29,30,31,33,34,36,42,46,49,50,56,58,63,65,67,73,76,81,83,89,103,109,115,120,122,130,132,136,138,139,148,149,150,152,156,159,161,162],printresnam:77,prior:[27,73,81,108,159,162],priori:159,prioriti:[17,24,150],privat:[3,6,10,17],privileg:[24,144],pro:[143,161],prob:104,probabl:[0,24,29,34,39,41,104,117,120,126,127,133,152,159,162,164],probe:[16,58,101,148,160],problem:[3,4,7,10,11,17,24,33,34,41,50,106,124,133,135,145,151,158,159,160,161,162,163,164],problemat:[6,155,158,162],proce:[16,40,124,133,158],procedur:[24,28,44,63,98,111,114,125,159,160],process:[1,3,4,16,20,21,63,75,76,87,124,130,132,150,152,156,158,159,160,161,162,164],processor:[24,130,137,142,150,152,158,159,161,162],prodrg:[151,163],produc:[0,2,3,4,6,9,12,19,20,21,24,28,34,36,42,45,50,52,53,58,62,63,76,80,93,94,95,98,100,103,104,127,128,130,132,136,137,145,148,150,151,152,155,159,161,162,163],product:[0,4,24,27,45,68,81,97,104,109,128,133,159,161,163,164],prof:155,profession:161,profil:[0,5,41,43,120,159],program:[0,2,4,12,16,17,25,27,29,32,33,34,46,48,49,50,52,53,56,58,60,63,65,66,68,71,74,76,81,85,87,96,101,103,106,108,109,113,114,115,116,117,119,120,122,123,124,130,132,138,143,150,151,153,155,156,161,162],programm:4,programmat:16,progress:[114,133,134,158],proj:27,project:[10,24,27,73,76,151,152],prompt:[27,56,73,83,87,124,148],promt:124,pronounc:161,propag:[4,10,161],proper:[4,7,10,108,122,124,130,138,152,159,162,164],properli:[24,34,42,76,108,120,125,126,145,149,150,156,162,164],properti:[41,48,49,56,57,67,89,124,139,140,159,162,163,164],proport:[24,27,28,60,66,129,159],propos:18,proprietari:161,prot:101,protect:[0,3,124],protein:[26,32,34,37,41,46,52,55,62,66,71,73,74,76,77,80,85,87,94,96,101,104,106,108,111,114,115,116,124,126,133,134,149,151,152,154,155,156,157,159,162,163,164],protocol:152,proton:87,prototyp:10,protrud:164,protsqueez:160,provdi:137,provid:[0,2,3,4,5,6,7,9,10,12,16,19,20,21,23,24,31,33,41,47,51,56,58,59,62,71,74,76,80,81,86,93,96,98,101,103,111,112,114,116,120,123,124,130,134,142,145,148,151,152,155,157,158,159,160,161,162,164],prune:[140,150,161],pseudo:[6,43,159],psi:[34,67,92],pthread:[10,161],ptr:155,ptrh:155,ptx:[134,143,150],pub:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164],publicli:[3,6],publish:156,pull:[35,76,120,125,131,139,150,161],pullf:[76,116,120,128],pullx:[76,116,120,128],puls:[150,159,161],pure:[10,28,38,44],purpos:[1,3,6,9,16,52,68,104,150,153,155,156,159,161,162],push:[3,10,20,160],put:[0,3,5,6,7,9,11,53,73,106,114,130,152,159,162,164],pygment:24,pymol:[24,84],python2:137,python3:137,python:[0,2,5,6,20,21,24,136],qcorr:81,qmbasi:159,qmcharg:159,qmmethod:159,qmmm:159,qmmmscheme:159,qmmult:159,qstep:100,quad:45,quadrant:24,quadro:[24,161],quadruplet:29,quadrupol:45,qualifi:[3,10],qualiti:[1,24,31,128,149,161],quant_corr:81,quantifi:162,quantiti:[0,32,104,114,127,138,140,159,160,161],quantum:[56,81],quarter:161,quartet:59,quasi:[27,159],quasiharmon:[27,73],queri:[142,158],question:[3,17,23,24,25,157,158,162,163],queu:160,queue:160,quick:[1,7,19,33,116,125,152],quickli:3,quiet:[16,25,137,148,150],quieter:[3,134],quit:[2,3,11,24,25,41,161,162],quot:[6,7,16,25,73,124,150],r_0:[51,117],r_i:64,r_ij:132,race:0,rad:[34,122,159,160],radacc:73,radcon:73,radeon:143,radfix:73,radial:[25,32,42,85,93,136,148,159],radian:[34,159],radii:[33,53,58,64,71,89,106,116,159,161,163],radiobutton:152,radiu:[25,51,53,58,60,64,66,67,68,71,73,89,101,106,115,148,151,159,160,162],radstep:73,rahman:[63,139,140,152,159,162],rai:[25,34,87,102,148],raii:10,rainbow:123,rais:159,rama:[25,34,148],ramachandran:[25,34,148],raman:66,ramomega:34,ran:[24,144],random:[20,25,27,28,35,58,60,61,71,76,82,88,100,120,128,132,148,152,153,158,159,160,164],randomli:[60,61,71,82,120,159,163],rang:[24,31,53,62,66,93,114,123,125,128,130,133,134,139,140,149,150,151,152,155,159,164],rank:[24,25,73,76,116,132,134,142,148,149,150,158,159,160,161],raphson:0,rapid:24,rapidli:158,rare:[7,9,16,21,24,130,139,151,158],rasmol:[27,32,37,53,114,115,150],rate0:159,rate:[28,66,139,142,159,161],rather:[0,3,4,10,24,29,34,36,44,45,46,49,52,53,55,56,58,62,68,101,126,127,128,130,132,150,153,156,159,162,163,164],ratio:[25,31,57,148,159,161],rational:[3,6,11],ravg:56,raw:[10,35,70,136,148,163],rbin:[66,107,117],rcmax:45,rcon:[76,161],rcoulomb:[116,128,135,149,150,152,155,159],rdd:[76,161],rdf:25,rdf_cn:93,rdist:124,rdtscp:24,reach:[12,24,61,73,76,89,126,159,160,162,163],reaction:[40,44,45,120,125,139,149,159],read:[0,3,10,19,24,27,28,29,30,32,33,34,35,36,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,63,64,65,66,67,68,70,71,72,73,74,75,76,77,79,80,83,85,86,87,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,106,107,108,109,110,111,112,113,114,115,117,118,119,120,123,124,128,139,145,148,150,151,152,153,157,159,161,162,163],read_first_x:138,read_first_xtc:152,read_next_xtc:152,readabl:[0,10,11,25,50,148,152],reader:[3,11,152,156],readi:[24,138,152],readm:12,readpul:133,readxtc:152,real:[0,16,17,24,26,27,28,29,31,33,34,35,36,38,40,42,43,44,45,46,47,49,51,52,53,54,55,56,58,59,61,62,63,64,66,70,71,72,73,75,76,77,78,79,81,82,84,86,87,88,90,93,94,95,97,99,100,101,102,104,105,106,107,108,109,110,111,114,115,116,117,118,119,120,121,122,123,124,133,151,152,153,159,161],realis:133,realiz:162,realli:[10,12,24,130,143,145,151,156,159,164],realloc:128,reason:[3,4,5,10,11,19,23,24,40,116,119,123,124,145,149,150,151,159,161,162,164],rebas:[21,130],rebuild:19,rebuilt:19,recal:162,recalcul:83,receiv:[24,76,126,161],recent:[24,76,125,126,127,130,132,134,137,140,141,142,149,151,158,161],receptor:72,recip:[49,118,164],reciproc:[0,76,88,116,159],recogn:[10,124,128,133,148,150],recognit:156,recommend:[3,24,58,60,61,63,81,114,134,137,142,151,159,161,162],recompil:24,reconfigur:24,reconsid:162,reconstruct:164,record:[29,53,87,96,101,114,146,147,150,152],recov:[4,52],recover:4,rect:114,rectangular:[53,114,138,152,159],recurs:21,red:[123,152,161],redhat:[24,126],redist:161,redistribut:[158,161],redmin:[1,8,10,18,20,21,23,130,141,146,147],redo:159,reduc:[0,10,24,28,33,39,43,57,108,114,117,128,131,132,134,137,145,149,152,159,162],reduct:[125,126,150,158,159],ref:[1,39,63,86,93,98,114,120,138,141,142,152,159],refactor:[5,7,130],refat:109,refcoord:159,refer:[0,1,2,3,9,10,12,19,23,24,25,32,37,39,41,47,55,56,57,58,59,63,71,73,80,85,86,90,93,94,95,96,98,101,103,107,109,112,114,115,124,132,133,137,139,145,149,150,151,155,157,159,160,161,162,163,164],referenc:[3,11,125],refgroup:86,refin:155,reflect:[3,125,126,141,142,158,159],reform:66,reformat:[6,7,8,20],reformat_al:[6,20],refrain:17,refus:[21,24,137],regard:[66,152,157],regardless:164,regener:158,region:[4,10,34,40,73,108,139,148,159,164],regist:[0,134,139],regress:[0,12,19,20,23,24,28,80,130],regressiontest:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164],regressiontest_download:0,regressiontest_path:[0,24],regressiontests_md5sum:2,regressiontests_tarbal:2,regtest:9,regular:[76,114,124,158],regularli:[155,161],reichold:164,reidel:156,reinterpret_cast:10,reintroduc:148,reject:[1,73,132,159],rel:[3,7,16,24,28,31,33,41,53,58,68,87,124,133,138,159,162,164],relat:[0,1,3,6,8,10,12,16,17,19,23,28,73,80,126,128,137,138,149,150,152,156,159,160,161,162,164],relax:[10,41,44,150,159,160,163,164],releas:[0,2,3,4,10,23,48,130,131,140,161],releng:[8,9,14,15,20,23],releng_path:[13,14,15],relev:[3,12,19,20,23,24,85,141,149,159,160,161,162,164],reli:[9,10,16,24,31,114,143,151,153,161,162],reliabl:[24,40,114,151],reloc:[16,24],relocat:[0,8,23],relwithassert:[0,4],relwithdebinfo:0,remain:[2,3,11,20,24,35,63,87,114,116,124,126,130,134,138,159,161,164],remaind:[125,158],remark:162,remd:[113,133],remdih:122,remedi:162,rememb:[36,159,164],remnant:145,remot:[76,158],remov:[0,3,6,21,24,36,38,40,41,53,54,57,62,63,71,76,80,87,98,106,111,113,117,119,122,128,139,143,146,148,149,151,152,158,160,164],renam:[5,6,7,11,24,74,76,125,141,148,150,158,159,162],render:84,renum:[63,87],renumb:[53,60,63,87,150],reorder:[35,87,115,150],reorgan:133,repeat:[0,3,10,35,116,126,159,160],repeatedli:24,repetit:11,replac:[3,6,21,61,71,120,126,132,134,135,137,145,148,159],replex:[76,160],replic:[20,138],replica:[76,129,134,159],report:[0,4,6,8,9,10,18,19,21,23,24,56,126,129,130,138,140,144,146,147,150,156,159,161],repositori:[0,5,8,9,12,14,15,20,21,23,24],repres:[3,28,53,68,93,101,120,151,153,159,161],represent:[6,43,73,114,121,150,153],reprod:[76,158,160],reproduc:[17,76,128,130,132,145,150,157,164],reprodud:158,repuls:[105,159],request:[0,9,24,56,63,76,83,112,128,132,134,136,137,148,159,161],requir:[0,2,3,6,8,9,10,12,16,19,21,24,27,32,35,39,40,53,63,66,68,72,73,76,98,101,102,104,108,109,114,116,124,126,127,128,135,136,142,148,150,151,155,159,160,161,162,163,164],rerun:[4,25,76,116,130,148,150,151,159,160],res:[51,86,93,96,114],res_cog:[47,58,59,71,86,93,101,103,112,124],res_com:[47,58,59,71,86,93,101,103,112,124,148],resarea:101,rescal:[152,159],rese:[76,160],research:[25,163],resembl:[11,28],reserv:[11,124],reservoir:158,reset:[0,116,126,128,138,159,161],resethwai:[126,161],resetstep:[116,126,161],resid:[3,8,148],residu:[25,32,34,48,53,55,60,61,66,67,68,71,74,75,77,86,87,92,95,96,101,103,106,114,121,122,126,128,136,138,148,150,151,152,155,159,164],residuetyp:87,resindex:[126,148],resiz:160,resnam:[99,103,124],resnr:[53,99,103,126,148,152],resolut:[137,150,159],resolv:[2,16,24,34,63,87,125,126],reson:[148,162],resouc:23,resourc:[10,24,134,147,161],respect:[3,6,7,10,11,18,21,24,28,32,39,41,65,77,79,81,87,93,94,96,104,114,116,120,124,125,130,148,150,151,159,160,161,162],respertim:77,respons:[10,11,16,40,96,134,160,162],rest:[3,29,34,35,106,159,160,161],restart:[63,73,80,120,127,128,131,151,157,159],restor:[126,137,158,161],restr:46,restrain:[73,128,138,159],restraint:[25,46,50,62,63,83,87,148,150,151,156,159,160,161,162,163,164],restran:34,restrict:[10,24,106,120,124,139,159,161],restructuredtext:[2,12],result:[0,2,3,4,9,10,16,17,19,21,24,26,28,31,35,40,52,58,62,63,66,71,73,76,81,86,101,106,110,114,116,122,124,125,126,128,130,134,136,137,138,143,145,150,151,153,158,159,161,162,164],ret:[51,152],retain:158,reus:[10,159],reusabl:19,rev:[9,21,110],reveal:[6,7,16,24,161],revers:[127,159],revert:21,review:[1,5,10,18,20],revisit:164,rewind:145,rework:[11,128],rewrit:3,rewritten:[16,148],rgb:[36,152],rgbhi:36,rgblo:36,rgbradii:159,rhel:24,rhf:159,rhist:51,rho:[94,110],rhombic:[53,114,161,164],rhosc:94,rid:16,ridden:24,ride:150,right:[3,17,19,35,123,124,129,138,152,159,160,161,162,163,164],rigid:[135,159],ring:87,rise:[67,68,159,162],risk:[24,130,133],rkappa:51,rlist:[128,135,149,155,159],rm2:159,rmax:[42,93,107,109,116,117,148],rmcomm:80,rmdh:54,rmin:[53,61,107,109,116],rmpbc:[47,58,59,86,93,101,103,112],rms:[25,26,35,67,79,95,123,148],rmsd:[25,26,33,35,37,52,56,73,79,83,94,95,98,148,152,159,164],rmsdev:96,rmsdist:[25,148],rmsdmir:94,rmsf:[25,27,148,164],rmsmean:95,rmsmin:35,rmsscale:95,rmvsbd:63,robust:[10,16,120],rocm:[24,161],rolandschulz:21,role:[11,164],roman:152,room:164,root2:123,root:[0,3,12,13,14,15,16,24,27,37,64,80,94,95,96,123,144,159,164],rot0:121,rot:[60,71,94,108,114,159],rotacf:[25,148],rotam:[29,34],rotangl:[76,116],rotat:[25,27,40,45,52,53,60,68,71,76,82,84,87,94,97,98,108,111,116,119,121,138,148,152,161],rotmat:[25,148],rotref:63,rotslab:[76,116],rottorqu:[76,116],rotxi:[98,114],rough:[33,159],rougher:93,roughli:[0,24,58,142,149,159],round:[114,122,125,129,138,151,152,153,162,164],routin:[3,4,10,12,24,40,53,128,130,131,132,133,136,151,152,159],row:[53,123,152,159,161],rpath:[16,24,143],rpo:125,rst:12,rsync:158,rt41c5:152,rtol:159,rtp:[87,122,150],rtpi:159,rtpre:87,rtti:10,rudimentari:0,rule:[5,10,11,12,18,20,28,73,124,150,152,159,162],run:[0,2,3,6,9,10,12,16,17,18,20,21,24,26,27,30,33,36,38,39,41,43,45,46,49,50,53,56,61,63,65,66,67,68,70,73,74,76,78,81,83,85,87,88,89,90,92,97,99,100,108,109,114,116,119,120,126,131,132,133,134,137,139,140,143,149,151,154,157,158,163,164],runav:[76,116],runavgdf:56,rundir:76,runtim:[24,38,143,150,159,161],rvdw:[53,116,135,149,150,152,155,159],rvec:[130,152],ryckaert:[29,78],s_a:31,s_b:31,s_idealga:56,sadli:24,safe:[4,10,24,40,125,150,158,161],safer:[129,138],safeti:[0,162],sai:[10,24,31,41,145,162,164],salt:[25,61,148,159],saltbr:[25,148],saltconc:159,sam:[73,76,116],same:[0,2,3,4,6,7,9,10,11,12,16,19,21,24,26,27,28,31,35,37,39,45,47,48,53,56,59,61,63,66,68,76,86,87,93,103,104,107,109,110,111,114,116,120,122,125,126,127,128,131,133,137,138,142,145,148,150,152,156,158,159,160,161,162,164],sampl:[20,25,27,31,56,73,76,104,116,120,137,139,140,148,156,159,164],san:[25,148],sander:[101,156],sandi:24,sanit:[0,24],sas:48,sasa:[25,148],satisfi:24,satisfiex:124,save:[10,24,49,114,150,158,159,163],sax:[25,148],scalar:137,scale:[28,41,42,45,53,71,73,81,93,94,95,106,111,116,117,118,119,123,131,134,138,149,150,152,159,160,161,164],scalefac:54,scalevdw:116,scan:[7,9],scatter:[25,148],scd:85,scdist:109,scenario:[2,41,76,164],scf:150,scharf:101,schedul:[126,158,161],scheek:73,scheme:[23,24,73,76,104,125,137,139,140,145,150,151,152,155,157,159,160,161],schlitter:27,scienc:158,scientif:[146,153,161,163],scientist:153,scl:95,scm:20,scope:[6,11,130,162,164],scount:[48,107],screen:[63,81,119,162],screw:122,script:[0,2,3,5,7,8,9,12,16,17,20,23,24,124,133,136,139,150,155,162],scroll:24,scum:107,sdf:108,sdk:24,search:[0,12,16,24,50,76,86,87,134,138,139,148,150,151,153,158,160,161,162,164],second:[1,3,19,28,37,42,44,52,56,59,66,68,76,79,86,89,94,103,104,109,114,123,124,130,138,150,152,159,161],secondaccessor:3,secondari:[25,48,77,148,152,156,164],section:[0,1,3,4,6,12,17,18,21,24,33,61,124,125,127,128,141,148,150,151,158,160,161,162,164],sed:7,see:[0,2,3,4,5,6,7,8,9,10,12,13,14,15,19,20,21,24,28,31,51,52,56,59,62,63,66,67,70,71,74,75,76,79,81,85,86,94,101,104,110,111,114,120,124,130,133,134,136,139,140,148,150,151,152,155,156,157,158,159,160,161,162,163,164],seed:[35,58,60,61,71,76,82,88,100,120,158,159,160],seek:[116,161,163],seem:[10,128,130,132,136,159],seen:[77,124,128,134,162],segfault:[128,145],segment:[10,39,108,137],segv:[36,138],sel:[66,86,93],select:[0,3,19,24,25,27,29,35,37,42,46,47,53,54,55,56,58,59,66,70,71,73,74,76,79,81,82,83,84,85,86,87,92,93,94,99,101,108,109,111,112,114,115,117,120,122,123,128,130,132,136,150,158,159,160,161,162,163],selectioncollect:19,self:[3,24,88,162],selgroup:86,selrpo:[47,58,59,71,86,93,101,103,112,124],seltyp:[47,59,86,93,103,112,124,148],semi:7,semicolon:[24,124],semiisotrop:159,send:[18,122,133,161],sens:[11,19,28,33,46,103,121,138,149,158,159,161,164],sensibl:162,sensic:101,sensit:[4,10,17,130,139,140,159],sent:76,sentenc:141,sep:[99,114,155],separ:[0,2,3,4,5,6,7,9,11,12,19,20,24,27,28,29,34,35,36,37,45,48,55,59,63,70,76,77,86,87,99,104,114,116,123,124,126,132,134,138,148,150,152,155,156,158,159,160,161,162,164],separate_dhdl_fil:31,seper:159,seph:155,septemb:128,sequenc:[9,24,67,76,121,152,159],sequenti:[95,161],ser:95,seri:[23,31,58,128,129,139,140,160,161,162],serial:[134,161],seriou:[24,84,130,159,161,162],serv:[63,132,159],server:24,session:152,set:[0,2,3,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,24,25,27,28,30,31,32,33,34,35,36,38,39,40,42,44,47,48,50,53,56,57,58,59,63,66,73,74,76,80,81,82,83,84,86,87,88,93,95,96,101,103,104,106,107,108,109,111,112,114,115,116,117,118,120,122,123,124,125,126,128,130,131,133,136,139,141,143,144,145,148,149,150,151,152,155,157,158,159,160,161,162,164],setenv:48,setfoo:11,setq:5,settim:[54,113],settl:[36,131],setup:[2,10,21,24,74,120,133,134,149,150,152,159],seventh:159,sever:[0,2,3,5,16,20,21,24,32,34,35,54,71,73,107,113,116,120,124,125,128,131,133,138,140,150,152,154,158,159,161,162,163,164],sfactor:102,sfina:10,sgang1:70,sgang2:70,sgsl:85,shake:[36,159,164],sham:[25,148],shamlog:104,shanno:159,shape:[27,41,49,57,93,114,133,159,164],share:[0,2,3,8,10,12,19,23,24,71,106,125,131,134,143,151,156,158,159,161,163],shared_ptr:10,sharp:137,shear:[110,159],sheet:152,shell:[0,2,16,24,66,106,108,115,124,138,150,156,160],shift:[32,34,40,41,53,63,73,77,114,116,125,134,142,145,149,159,161,162,164],ship:24,shoot:164,shortcom:24,shorter:[28,118,121,139,161],shortest:[53,93,115,148,159],shortli:160,should:[0,1,3,4,5,6,7,9,10,11,12,16,18,19,24,27,28,29,31,35,39,40,41,42,44,47,48,49,52,54,55,59,60,61,66,68,71,76,81,84,85,86,87,89,90,96,100,101,106,107,110,113,114,116,118,120,124,125,126,127,128,130,132,133,136,137,139,141,145,148,149,150,151,152,153,155,156,158,159,160,161,162,163,164],shouldn:[156,158,159,164],show:[0,2,3,6,9,12,16,19,27,28,50,96,103,104,119,123,128,131,142,148,149,152,161,164],show_bug:126,shown:[6,17,19,152,159,162],shrink:160,shuffl:[35,148],side:[0,6,12,24,40,41,53,73,90,131,134,143,152,162],sidechain:[34,68,164],sig56:53,sig:105,sigep:[25,148],sigfac:105,sight:136,sigint:150,sigma:[25,28,53,54,81,105,120,148,150,159],sign:[24,61,73,159,162],signal:[76,138,150,158],signifi:6,signific:[3,24,94,134,148,159,160,161,162],significantli:[0,3,24,53,86,126,131,139,148,158,161,164],sigterm:150,sigusr1:150,silenc:[6,130],silent:[10,126,129],silli:164,silver:24,sim:[56,159],simd:[0,6,10,131,140,149,150,161],similar:[3,4,5,6,10,16,21,24,38,53,94,111,120,134,156,159,160,161,162,163,164],similarli:[3,24,33,59,76,91,127,130,131,133,148,160,164],simpl:[3,6,10,19,87,92,103,105,106,120,136,152,159,161,162],simpleaccessor:3,simpler:139,simplest:[24,149],simpli:[3,16,41,56,60,63,67,84,106,108,113,116,124,128,148,152,153,159,162],simplic:[24,150],simplifi:[24,126,134,148,151,164],simul:[0,4,10,17,23,24,31,33,35,36,40,41,44,45,49,51,56,58,63,72,73,76,77,80,81,116,120,122,128,131,139,140,142,149,150,152,155,157,161,163,164],simultan:[55,114,123,150,159,161],sin:[29,104],sinc:[0,2,3,4,6,10,12,24,27,28,40,41,48,57,58,62,73,82,84,87,97,98,100,106,108,113,125,126,127,128,129,130,131,133,136,137,138,140,141,142,143,144,145,149,150,156,158,159,160,161,162,164],sine:110,singl:[0,3,5,6,11,12,23,24,27,34,35,45,47,51,56,58,59,62,66,71,73,76,86,87,93,101,103,104,112,114,123,124,126,128,129,132,136,137,138,140,142,145,148,149,151,157,158,159,160,162,164],singular:159,sinh:110,sit:164,site:[9,22,24,33,63,81,87,106,130,149,153,159,161,162],situat:[3,128,130,159,160,162,164],six:[82,84,159,161],size:[0,10,24,25,28,35,36,41,42,53,58,64,68,71,76,93,94,103,106,108,114,123,124,126,128,130,134,136,137,138,145,148,149,150,151,152,156,159,160,161,163,164],skip2:94,skip:[0,3,6,27,28,30,35,36,45,55,56,83,94,98,104,114,123,137,138,145,150,152,159,161],sksl:85,skylak:[24,140],slab:[45,159],slant:164,slash:156,slice:[41,45,64,65,85,90],slight:[138,143,158,159,161],slightli:[24,87,124,134,142,150,159,160,162],slope:[73,162],slow:[19,24,45,73,87,117,131,150,159,161,162],slower:[24,124,128,130,149,159],slowli:[1,23,24,161],slurm:24,sm_37:137,sm_60:[125,134],sm_61:134,sm_70:137,small:[10,25,34,35,41,43,60,71,93,106,114,124,125,128,129,130,133,134,138,141,143,148,149,150,151,155,159,160,161,164],smaller:[17,24,33,67,73,76,86,116,130,136,139,148,152,159,160,163,164],smallest:[35,75,115,161],smart:[10,113],smear:41,smi:[24,161],smooth:[25,35,44,57,114,120,123,148,150,159],smoothli:[1,35,159],smt:161,snc:24,snew:10,snor:107,soc:156,socket:161,soft:[150,159,164],softwar:[17,24,125,151,152,155,156,161,163],sol:[55,124,152,159,162],sole:[0,63,150],solid:[148,159],solut:[3,24,25,53,71,106,107,108,109,128,130,133,145,148,155,156,161,162,163,164],solv:[9,16,17,126,150,159,161,162,163],solvat:[25,71,101,108,148,149,151,156,159,160,162,163,164],solvent:[25,38,48,61,66,71,72,101,106,107,108,109,128,138,148,149,150,151,156,160,162,163,164],solver:[53,159,164],some:[0,1,2,3,4,5,6,7,8,9,10,11,12,16,17,19,20,21,23,41,53,55,56,58,63,73,76,86,87,103,108,114,119,120,124,127,128,129,131,132,133,134,137,139,140,141,145,146,148,150,151,152,153,155,158,159,161,163,164],somebodi:[130,136],someclass:3,somehow:1,someon:[1,7],someth:[3,20,113,130,133,145,151,158,159,161,162,164],sometim:[24,87,128,151,153,156,159,161,162,164],somewhat:[3,116,122,137,139,148,153,159],somewher:[19,127,149,156,158,162,164],soon:[124,133,147,159],sophist:[106,120],sord:107,sori:107,sorient:[25,148],sort:[7,20,26,54,113,124,128,138,148,161,163,164],sorter:[6,7,20,21],sourc:[2,3,5,7,8,10,11,16,18,19,20,23,24,130,132,133,145,150,153,158,160,161,162,164],source_md5sum:[0,2],source_tarbal:2,space:[5,24,29,31,34,42,60,71,73,88,100,108,114,116,117,120,139,148,150,152,159,161,162],spam:126,span:[40,97,124,159],sparc64:24,sparc64_hpc_ac:24,sparc64viiifx:24,sparc:[0,24],spars:136,spatial:[25,43,138,148,161],spc216:[106,151],spc:[45,87,106,152,162],spce:87,speak:11,speci:[133,151,162,164],special:[8,9,10,23,48,53,74,87,124,130,150,151,152,157,159,161,162],specialist:24,specif:[0,1,2,4,7,9,10,16,18,19,20,23,24,46,62,80,92,114,130,149,150,151,159,161,162,163],specifi:[0,3,6,9,20,21,24,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,126,129,133,136,138,139,148,149,150,152,156,158,159,160,161,162],speckl:108,spect:[43,70],spectra:[25,100,118,148],spectroscopi:66,spectrum:[49,81,118],speed:[3,24,124,134,148,153,158,159,161,164],speedup:142,spell:11,spend:153,spent:161,sphere:[58,59,101,152,159],spheric:[90,161],sphinx:[0,2,12,24],sphnorm:59,spike:[137,164],spline:150,split0:159,split1:159,split:[4,5,8,23,27,31,64,74,77,80,88,89,94,101,109,114,148,150,159,161,162],spme:[88,159],spoel:[34,120,159,164],spol:[25,148],spontan:73,spread:[130,152,161],spring:73,spuriou:[132,159],sqframe:100,sqrt:[27,28,30,53,64,67,81,110,117],squar:[0,24,25,27,28,35,37,39,40,49,56,64,79,80,89,94,95,96,98,148,152,159,164],src:[0,3,4,7,10,16,19,21,159],srun:24,sscanf:132,ssdump:[34,48],sse2:[24,150],sse4:[24,150],sss:48,stabil:163,stabl:[108,151,159,164],stabli:164,stack:[0,3,4,17,24,60,106,161],stackoverflow:5,stage:[24,158,159,160,161,163],stai:[21,114,149,159,163,164],stamement:132,stamp:113,stand:[55,66,103,152,155,162],standard:[0,3,7,11,12,16,17,24,28,31,34,47,49,50,58,73,81,87,95,96,101,114,119,120,127,150,151,152,155,159,161,162,163,164],stare:161,start:[3,4,6,7,10,11,12,17,20,23,24,28,34,40,44,45,53,54,62,63,66,71,73,74,76,80,82,87,100,102,103,104,105,113,114,116,124,126,130,133,137,144,145,148,150,151,152,154,157,158,159,160,161,162,163,164],startq:[100,102],startup:[25,158,161],stat:[16,159],state:[11,25,31,33,49,50,53,55,56,61,76,87,116,126,129,138,148,150,152,158,159,163,164],state_prev:76,statement:[0,5,6,7,63,152,162],static_cast:10,statist:[26,31,34,40,47,54,56,80,116,120,127,138,139,140,150,159,161],statu:[19,24,132,151,162],std:[3,4,10,126,127],stddev:28,stderr:[4,6,76,132,137,141,159,161],stdev:31,stdin:19,stdio:[4,7,10],stdlib:24,stdout:[42,161],stead:152,steep:159,steepest:[132,159],steer:24,stem:88,step0:159,step:[24,35,38,39,45,46,52,56,57,63,67,73,76,81,100,108,114,116,125,126,132,133,135,137,139,141,142,148,149,150,151,152,154,156,157,158,159,160,161,164],stepsiz:73,steric:164,stesp:133,still:[2,3,4,6,11,16,21,24,33,36,41,63,93,108,124,125,126,127,128,130,131,134,138,139,144,145,148,149,150,151,158,159,160,161,162,163,164],stimul:73,stl:10,sto:159,stochast:[76,159],stock:24,stop:[5,24,28,54,66,76,120,136,150,152,158,159,162],storag:[136,158],store:[1,6,28,46,47,53,56,58,59,73,75,76,80,83,86,93,101,103,112,113,115,117,124,126,128,130,138,141,145,152,159],straight:[40,56,80,89,145],straightforward:[19,24],strain:159,strang:[91,130,145],strategi:159,stream:[10,150,161],strength:[73,159],strict:[10,130],stricter:[6,20],strictli:[11,124,150],stride:[124,161],string:[0,10,19,24,31,33,41,43,45,48,53,61,65,72,73,76,84,87,90,114,116,121,122,124,126,128,132,141,152,156,158,161],stringtest:19,stringutil:19,strip:[0,87],strive:24,strong:[24,131,142,152,161],strongli:[10,24,149],stroustrup:5,struct:[10,11,73,136,141],structur:[1,3,10,16,26,27,32,33,34,35,37,39,40,42,47,48,52,53,57,58,59,60,61,62,63,64,67,68,73,74,75,76,77,79,80,81,82,84,86,87,91,93,94,95,96,98,101,102,103,106,107,108,110,111,112,114,115,116,117,118,119,122,124,126,128,138,145,150,151,155,157,159,160,162,163],stryer:156,stuck:159,studi:[151,155,159,163,164],studio:[0,16,24],stuff:161,style:[1,3,5,6,7,8,9,10,21,23,24,128,138,156,160],sub:[114,123],subav:28,subbuild:9,subclass:3,subcount:[0,125,161],subdirectori:[2,3,6,12,19,24,31,87],subexpress:124,subfold:151,subgroup:[25,148],subinterv:103,subject:[20,21,23,24,41,159],submit:[17,18,20,158],subpag:3,subroutin:159,subsect:133,subsequ:[3,16,29,31,87,106,108,113,114,125,152,159,162],subset:[10,12,23,38,101,114,116,124,130,131,160,161],subspac:[27,73,82],substanti:[41,49,120],substat:5,subsystem:[24,159],subtitl:31,subtleti:3,subtop:124,subtract:[28,45,56,81,87,109,124,128,129,138,149,159,164],subtrajectori:114,subunit:159,succe:[0,20,164],success:[0,16,138,152,158,163,164],successfulli:[0,24,130,161],suddenli:162,sudo:24,suffer:161,suffic:[116,159],suffici:[1,3,49,61,76,108,116,120,126,156,159,162,163,164],suffix:[0,3,11,21,24,158,160],sugar:155,suggest:[10,24,66,76,108,114,124,128,132,141,144,162,163],suit:[0,19,20,24,114,126,140,142,148,155,159,163,164],suitabl:[0,4,6,12,16,24,62,72,86,126,128,148,151,152,155,161,163],sulfat:61,sulfoxid:156,sulfur:151,sum:[0,9,28,33,39,42,55,56,58,71,83,90,98,106,107,114,116,125,128,145,150,153,159],sum_i:[64,67],sum_k:159,sumh:95,summar:33,summari:[9,19,150,157,159,161],summat:[24,40,138,145,158,159],superimpos:[35,37],superior:134,superposit:[37,94,96],supersed:144,suppli:[27,28,33,34,35,42,55,63,72,74,94,95,96,104,114,122,123,133,145,148,149,151,152,156,159,160,162],support:[0,3,6,10,12,16,18,19,31,59,63,87,93,106,114,116,120,122,124,129,131,140,143,146,147,148,149,150,151,152,155,159,164],supportlevel:126,suppos:[155,156,164],suppress:[4,9,12,57,123,151,162,163],sure:[4,10,17,24,28,57,76,80,87,96,108,110,118,145,159,160,161,162,164],surf:93,surfac:[25,41,43,48,93,101,104,108,148,150,159,162],surround:[1,40],suspect:76,suspend:[158,160],sustain:159,swap:[76,116,159,161],swapcoord:159,swapion:[76,116],swift:48,swiss:151,swissparam:163,sym:120,symbol:[0,5,10,11,16,148],symm:41,symmetr:[24,41,120,159],symptom:164,symptomat:164,sync:[2,8,136],synchron:133,synchroni:128,synonym:124,syntact:124,syntax:[6,48,103,128,162],sys:[24,50],system:[2,4,6,7,8,9,12,16,17,23,24,25,31,36,40,41,45,49,50,53,61,63,71,73,74,76,80,85,87,101,108,114,116,120,125,127,128,129,131,132,133,134,135,136,138,142,145,148,149,150,152,153,155,156,157,158,159,160,161],systemat:[116,128,139,160],szonli:85,t_exampl:3,t_struct:3,t_sym:159,tab:[3,5,12,120],tabl:[34,76,116,122,134,149,160,161,164],table_na_cl:159,table_na_na:159,tableb:[76,116],tablep:[76,116,159],tabul:[76,120,128,142,149,150,159,161,164],tag:[3,6],tail:[25,44,52,85,138,148],take:[1,3,4,19,24,31,35,36,41,45,52,63,65,71,73,77,81,90,108,116,124,125,133,134,139,148,149,150,151,159,160,161,162,164],taken:[24,27,28,34,39,40,42,54,61,73,82,90,94,95,96,113,114,116,122,123,124,125,126,127,128,129,137,139,159],tangenti:43,tape:114,tar:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,12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ustify_onli:21,uncrustifymod:21,uncrustifypath:21,undef:63,undefin:[10,95,124],under:[0,3,6,7,9,10,18,19,20,21,24,73,76,125,130,146,149,150,151,158,159,160,161,162],underestim:[120,129,159],undergo:114,underli:[0,148,162,164],underscor:[11,76,152,159],understand:[1,3,6,8,10,11,12,16,19,20,23,24,146,153,161],understood:[4,159],underwai:158,undesir:151,undo:164,undocu:[3,6,135,136],undoubtedli:162,undul:41,undulatori:41,unequ:124,unescap:3,uneven:159,unexpect:[4,16],unfinish:6,unfold:40,unfortun:[24,147,153,159],unifi:151,uniform:[3,114,133,150,159,162],uniformli:[134,159],unilater:126,unimpl:127,uniniti:[126,158],unintend:17,unintention:3,unintuit:124,union:[124,159],uniq:138,uniqu:[11,16,41,76,87,103,116,124,162],unique_cptr:10,unique_ptr:10,unistd:7,unit:[0,8,10,12,18,20,23,24,27,29,30,31,32,34,35,36,39,40,41,42,43,44,45,46,47,48,49,51,55,56,57,58,59,64,65,66,67,68,70,72,75,77,80,83,85,86,87,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,107,108,109,110,111,112,113,114,115,117,118,119,120,123,128,129,130,134,148,149,150,155,159,161,164],uniti:0,unitless:159,univers:145,unix:[24,92,152,156,158],unknown:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164],unless:[3,4,7,10,11,16,24,27,53,63,76,106,114,126,128,138,145,148,149,151,159,161,162],unlik:[80,126],unlimit:[38,158],unmaintain:23,unmodifi:[3,159],unnam:3,unnecessari:[7,10,11],unnecessarili:[3,11,12],unorgan:7,unpack:24,unphys:[52,79,159,164],unproblemat:128,unproton:87,unrealist:[84,162],unreason:17,unrel:7,unreli:158,unrestrict:24,unsat:85,unsatur:85,unset:124,unstabl:[3,6,9,63,141,157,159,162],unsuccess:125,unsuit:163,unsupport:[143,161],unsur:159,until:[16,24,28,29,33,34,38,40,45,49,56,64,66,71,97,110,118,150,152,158,159,160,161,162,163],untrap:4,unus:[159,161],unusu:120,unwant:[159,162],unwis:75,updat:[5,8,9,10,20,21,24,54,61,73,114,128,131,134,137,140,150,152,159,160,161,162],upgrad:133,uphil:35,upload:9,upon:[0,24,76,148,150,151,152,160],upper:[11,35,62,123,159,160],uppercas:[11,124,136],ups:5,upscal:116,urea:152,usabl:[3,11],usag:[0,6,7,9,12,18,41,48,49,108,117,143,150,151,156,157,161],use:[0,1,2,3,4,5,6,7,8,9,10,11,12,16,17,18,19,20,21,24,27,29,31,32,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,53,54,55,57,58,59,61,63,64,65,66,67,68,70,71,72,73,74,75,76,77,80,82,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,107,108,109,110,111,112,113,114,115,116,117,118,119,120,122,124,125,127,128,131,132,134,136,137,138,139,140,142,143,144,145,148,150,151,152,155,156,157,158,159,160,161,162,163,164],useabl:159,used:[0,2,3,4,6,7,8,9,10,11,12,16,19,20,21,23,24,25,27,29,33,34,35,36,37,39,40,41,44,45,46,48,50,52,53,54,55,59,60,62,63,65,66,73,76,81,83,85,86,88,89,93,98,101,103,104,106,108,110,111,113,114,115,118,119,120,122,124,125,126,128,129,130,132,133,134,138,139,140,141,142,144,145,148,149,150,151,152,156,158,159,160,161,163,164],useful:[0,2,3,10,16,17,19,23,24,25,27,28,33,37,38,50,53,55,57,62,66,74,76,77,87,94,98,103,109,114,115,120,124,125,127,131,133,134,135,136,137,139,140,141,144,145,148,150,151,152,155,158,159,160,161,163,164],usefulness:[71,106],useless:[50,129,130,141],user1:159,user2:159,user:[0,2,3,4,5,9,16,19,23,24,35,56,60,61,63,70,76,83,87,104,108,114,119,120,124,130,131,136,137,139,141,142,143,145,146,147,149,150,151,152,153,155,158,160,161,162,164],userint1:159,userint2:159,userint3:159,userint4:159,userreal1:159,userreal2:159,userreal3:159,userreal4:159,uses:[0,2,3,6,7,9,10,12,20,21,24,48,53,63,76,78,87,100,124,126,128,134,138,139,140,145,148,149,150,152,153,156,158,159,161,162,163],using:[0,3,4,5,6,7,9,10,11,12,16,18,19,20,21,23,24,25,26,28,29,31,33,34,35,36,38,40,41,45,46,49,52,55,56,57,58,61,63,66,71,76,80,81,88,89,97,98,100,106,108,110,114,118,124,126,127,129,132,134,136,139,142,144,148,149,150,151,152,155,156,157,158,159,160,161,163,164],usr:[16,24,48,116,156],usual:[24,31,34,42,49,63,76,80,89,104,108,130,139,143,149,151,152,156,159,161,162,164],util:[0,4,7,10,12,19,24,72,105,134,139,151,161,162,164],utilis:162,v23:107,vac:118,vacanc:[25,148],vacant:71,vacf:49,vacuo:[163,164],vacuum:[159,160],vale:104,valgrind:[12,19,145],valid:[3,10,24,52,63,94,108,124,130,133,140,141,151,158,159,162],valu:[0,2,3,4,9,10,11,16,21,24,27,28,31,32,33,34,35,36,37,39,40,41,44,45,46,47,48,49,51,53,55,56,58,59,64,66,71,72,73,76,77,78,80,81,83,86,88,89,91,93,94,96,100,101,103,104,106,108,110,111,112,113,114,116,117,122,123,124,126,127,130,133,134,136,143,145,148,149,150,151,152,156,158,159,160,161,162,164],valuabl:[24,138,153],van:[25,33,34,53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x2top","gmx xpm2ps","Selection syntax and usage","GROMACS 2016.1 Release Notes","GROMACS 2016.2 Release Notes","GROMACS 2016.3 Release Notes","GROMACS 2016.4 Release Notes","GROMACS 2016.5 Release Notes","Bugs fixed","Highlights","Miscellaneous","New and improved features","Performance improvements","Removed mdrun features","Improvements to GROMACS tools","GROMACS 2018.1 release notes","Bugs fixed","New and improved features","Highlights","Miscellaneous","Performance improvements","Portability","Removed features","Improvements to GROMACS tools","Release notes","Release notes for older GROMACS versions","Command-line reference","Non-bonded cut-off schemes","Environment Variables","Answers to frequently asked questions (FAQs)","File formats","Floating point arithmetic","Flow Chart","Force fields in GROMACS","Getting started","User guide","Managing long simulations","Molecular dynamics parameters (.mdp options)","Useful mdrun features","Getting good performance from <code class=\"docutils literal\"><span class=\"pre\">mdrun</span></code>","Common errors when using GROMACS","System preparation","Terminology"],titleterms:{"1x1":139,"29943f":130,"3dc":125,"case":[130,133,136],"class":3,"default":[125,136,138,162],"enum":3,"float":153,"function":[3,133,137,138,141,150],"import":156,"int":130,"long":[126,142,158,162],"new":[19,130,133,136,139],"null":128,"public":3,"return":138,"short":[143,161],"static":[9,24,126,127,132],"switch":128,"try":[126,133],Added:[126,128,129,130,132,133,134,136,137,138,139,141,142,143,145],Are:158,Doing:24,The:162,There:162,Use:142,Used:[134,136,137,138],Useful:160,Using:[3,21,24,152],abort:130,about:[126,138],acceler:[24,139,161],access:[24,128],account:129,accuraci:[125,129],activ:129,adapt:159,add:[126,130,132,134,136,142],adding:137,adress:135,advanc:24,affect:0,affin:130,after:[24,129,133],again:136,against:130,algebra:24,algorithm:[133,139,161],all:[0,128,130],alloc:162,allow:[10,133,141,145],alwai:[130,145],amber:155,amd:[127,137,142],anadock:26,anaeig:27,analys:145,analysi:[9,25,27,120,136,148,150,151],analyz:[25,28,127,148],andersen:[129,138],angl:[29,124,133,142],anneal:159,answer:151,api:3,append:[133,158],appli:138,applic:[130,144],arbitrari:148,arg:141,arithmet:[124,153],arm:[128,143],armv7:130,around:[127,128,130,132,137],ascii:138,ask:151,aspect:[24,128,141],assert:137,assign:[137,161,162],atom:[124,129,130,133,137,145,148,162],atomnam:124,attach:126,autocorrel:120,autom:[132,142],automat:[21,125,134],avail:143,averag:[137,164],avoid:[128,129,130,137,138,143,145],avx2:142,avx2_128:142,avx512:[127,128,137],avx512f:128,avx:[128,142],avx_512:143,awh1:137,awh:[30,137,139,159],axi:133,back:158,background:[156,161],balanc:[125,129,134,141],bar:31,base:124,basic:3,befor:138,behav:[126,127,128,129,137],behavior:138,berendsen:138,best:142,better:[136,141,161],between:[25,27,145,148,162],bia:137,bias:[139,159],big:130,binari:[16,24],bit:[130,142],block:[136,162],blow:164,bluegen:24,bond:[25,126,134,137,145,148,149,159,162],both:137,bottom:[126,128,133],bound:[125,162],boundari:[134,164],box:[137,162],bradlei:142,buffer:[130,138,139,142],bug:[125,126,127,128,129,130,137,138],build:[0,2,3,9,13,19,20,24,125,126,127,128,132],bundl:32,cach:[0,130,132],calcul:[27,126,130,133,137,145,159,161],call:[127,128],can:[136,162],cdt:5,cell:162,centr:137,chain:162,chang:[20,24,129,130,133,134,136,138,139,141,143,145,148,158,162],charact:[130,132],charg:[129,137,141,145,162],charmm:[129,145,155],chart:154,check:[33,126,127,128,129,130,132,133,136,137,138,141,143,145,161,162],checker:6,checklist:161,checkpoint:[129,132,133,158],chi:[34,145],choic:[129,138],choos:142,clang:[9,127,137,143],clarifi:[126,128,129,141,145],classic:159,clear:142,clock:[130,138,144],clock_gettim:132,cluster:[24,35,138],clustsiz:36,cmake:[0,24,143],cmake_cxx_flag:126,cmap:132,code:[0,1,3,5,11,12,20,21,22,125,126,128,130,134,143],codebas:12,com1:133,com:[128,129,133,138,145,159],combin:[129,134,138,143],command:[24,25,124,141,148],comment:[1,129,145],commit:[1,21],common:[3,11,162],commun:162,compact:135,comparison:[138,149],compat:[143,162],compil:[0,9,24,126,127,128,130,132,133,137,143],complex:145,compon:24,compress:133,comput:[133,159,161],concern:[1,151],condit:[126,142,164],configur:[24,134,161],confout:129,confrm:37,confus:[129,138],conjug:162,conserv:[139,164],consid:163,consider:[10,161],consist:128,constraint:[132,138,162],construct:3,content:128,continu:[138,144,158],control:[3,150,159,160,161],convent:[11,148],converg:162,convers:136,convert:[25,38,144,148],coord:[128,133],coordin:[25,133,134,148,162],copyright:21,core:[133,150],correct:[24,125,126,127,128,129,137,138,139,145],correctli:[126,137],corrrel:126,could:[126,127,128,129,137],count:133,counter:130,coupl:[133,134,137,138,139,159,162],covar:39,covari:[25,27,148],coverag:9,cpi:129,cppcheck:9,cpt:152,cpu:[134,137,144],cpuid:130,crai:24,crash:[126,137],creat:17,cross:126,cryptic:125,cube:137,cuda:[24,126,128,130,132,133,134,137,143],current:40,cut:[149,162],cutoff:[129,137,138],cycl:130,dat:152,data:[16,126,130],databas:[162,163],deadlock:125,death:137,debug:[130,150],decomposiion:137,decomposit:[129,161,162],decoupl:126,decreas:[145,162],defin:[137,159],demand:9,densiti:[41,136,145],densmap:42,densord:43,depend:[6,132],der:159,descript:[25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,128,141],detail:[6,152],detect:[127,130,133,137,138,142],develop:[8,12,17,20,23,130],devic:[134,138,143],diagnos:164,diagon:162,dielectr:44,differ:[129,137,145],difficulti:24,dihedr:[126,133,141],dihedral_restraint:128,dipol:45,direct:[7,137,162],directori:[3,133],dirti:24,disabl:[125,128,132,133,143],disallow:[126,129,138],displac:137,disr:46,dist:124,distanc:[25,47,124,125,148],distribut:[25,148],divid:137,divis:130,dlambda:[129,138],dlb:141,dlg:152,do_dssp:[48,127],doc:129,document:[2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:130,resid:124,residu:[124,145,162],resindex:124,resnr:124,restart:[130,133,137,158],restraint:[125,126,128,129,138,141,145],revert:130,right:24,risk:126,riski:108,rlist:162,rms:94,rmsdist:95,rmsf:[96,126],robust:137,rogu:127,rotacf:97,rotat:[128,159],rotmat:98,round:[139,145],routin:134,rsqrt:143,rtp:[145,152,162],rule:[1,3,134],run:[19,25,125,127,128,129,130,138,141,142,148,150,152,156,159,160,161,162],runtim:126,rvdw:[133,162],ryzen:142,s390x:126,saltbr:99,same:124,sampl:152,san:100,sasa:[101,136],sax:102,scale:[137,162],scatter:134,scheme:[128,130,134,135,138,142,149],scope:3,script:[6,21,125],sd2:135,search:[141,144,159],second:162,seed:136,seem:162,select:[103,124,126,137,145,148],sensit:136,separ:127,sequenti:162,seri:[146,147],set:[5,21,129,137,138,156],settl:[125,134,139,162],setup:[128,130,139,142,161],sever:[126,127],shake:[137,162],sham:104,share:[16,137],shebang:137,shell:[127,133,159],shift:128,shortest:162,should:17,shuffl:136,sigep:105,signal:[133,137,141],simd4:128,simd:[24,125,127,128,134,137,142,143],simpl:142,simplifi:136,simul:[25,125,130,133,134,137,148,151,156,158,159,160,162],singl:[130,161],site:[134,138],size:162,slower:125,sm_60:126,small:162,smallest:162,smt:137,softwar:162,sol:127,solari:[24,128],solid:124,solv:128,solvat:[106,127,128,136,138],solvent:[136,159],some:[24,126,130,136,138,162],sorient:107,sort:[6,136],sourc:[0,6,9,12,21,22],space:127,spatial:108,special:[0,24,148],specif:[3,25,148],specifi:124,spectrum:138,speed:142,split:[132,134,145],spol:109,spread:142,sqrt:128,src:12,standard:10,start:[19,156],state:[128,144],statement:[132,137],std:130,step:[130,138,145,162,163],stepsiz:162,stochast:141,stop:[126,138],store:133,stream:132,string:125,struct:3,structur:[24,25,148,152,156,164],style:[18,20],subdirectori:162,submit:[1,9],subset:[136,148],suggest:[125,133,164],suit:[25,139],sum:162,summari:152,summat:129,support:[17,24,125,126,127,128,130,132,133,134,135,136,137,138,139,141,142,161],suppress:6,surfac:125,swap:[128,133],symbol:143,synopsi:[25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123],syntax:[124,148],system:[0,20,126,137,139,151,162,163,164],tabl:[23,125,128,159],tabul:137,tarbal:9,target:[0,137],task:161,tau:126,tcaf:110,tdb:145,temperatur:[128,159],term:129,termin:[125,139],terminolog:164,tesla:125,test:[9,11,19,22,24,125,127,130,132,137,143,159],tex:152,text:[128,132,137,141,145],than:[161,162],thermostat:[130,164],thing:133,thingi:159,thread:[125,126,127,129,130,133,134,138,142],time:[20,25,125,126,138,145,148,162],tinyxml:130,tip:163,tips3p:[129,145],tng:[126,133,137,141,145,152,156],toler:138,too:[130,136,162],tool:[2,20,25,126,127,128,129,136,137,145,148],top:[152,156],topic:148,topolog:[25,137,148,152,156,162],total:162,tpbconv:148,tpi:137,tpr:[38,129,133,138,144,145,152,156,158],tpx:138,traj:[111,127,145],trajectori:[25,112,126,128,136,145,148,152,156],transform:[24,134],transit:144,transpos:134,tree:[6,24],trick:163,triclin:129,trigger:[13,143],trjcat:[113,138],trjconv:[114,126,145],trjorder:115,trr:[126,130,152,156],tumbl:137,tune:[128,134],tune_pm:[116,127],turn:126,tutori:156,tweak:142,twin:135,two:[130,162],type:[0,126,145,148,161],typic:[24,156],unambigu:137,unavail:[133,137],unbound:133,uncrustifi:[9,21],under:12,understand:9,unit:[11,19,132,136,142],unix:12,unmaintain:146,unstabl:164,unus:128,upcom:137,updat:[125,129,130,141,142,144],upgrad:132,upon:127,urei:142,usag:[124,137,145,148,162],use:[126,130,133,149],used:[137,143,162],useful:126,user:[12,125,126,127,128,129,133,138,157,159],using:[128,130,137,138,145,162],util:137,valid:139,valu:[128,137,138],van:159,vanhov:[117,126,136],variabl:[0,125,126,150],variou:132,vcm:139,vector:162,velacc:[118,138],veloc:[130,133,159],verif:9,verlet:[129,130,134,138,149],version:[24,133,137,141,142,143,147,148,161],view:[25,119,148],violat:126,virial:[125,127,137],virtual:[134,138],visibl:3,visual:151,vmx:125,volta:128,vsite:[130,133,141],vsx:137,waal:159,wai:137,wall:[125,126,129,137,138,159],warn:[108,125,126,129,132,133,137,138,145,162],water:[138,145],welcom:23,were:134,werror:126,wham:[120,125,130,136],what:[17,21,164],wheel:121,when:[125,126,129,132,133,137,138,142,145,162],where:[24,126,127,128,129,137],whose:137,wiki:128,window:[24,132],within:[124,161,162],without:[136,137,158],work:[125,127,128,130,132,133,136,137,143,145],workflow:[9,17,164],workload:134,write:[125,132,141,145],written:[125,133],wrong:129,x2top:122,x86:126,xeon:24,xlc:127,xplor2gmx:125,xpm2p:[123,126],xpm:152,xtc:[152,156],xvg:[127,152],xxx:162,yes:137,yield:127,your:[152,156,158],yyi:162,zen:[137,142],zero:[130,137,162]}})
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