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:112,monoton:109,mont:[30,82,94,118,125],more:[0,1,3,6,8,9,15,16,17,19,20,24,26,30,36,43,51,54,58,61,65,68,69,71,76,79,80,81,84,87,95,97,98,100,101,104,110,112,113,115,117,118,119,120,121,122,123,124,125,126],morokuma:125,morph:21,mors:125,most:[0,1,2,4,6,8,15,16,20,23,36,50,51,68,90,102,109,113,116,117,118,119,120,121,123,125,126,127],mostli:[0,1,3,13,20,118,120],motif:[20,112],motion:[21,23,31,52,75,78,81,107,125],move:[8,13,20,31,36,110,117,118,125,126],movi:[21,52,78,107,118],mp2:125,mpi:[0,4],mpi_barrier:120,mpi_sendrecv:120,mpicc:20,mpich:20,mpicxx:20,mpiexec:20,mpiexec_numproc_flag:20,mpiexec_postflags:20,mpiexec_preflags:20,mpirun:[20,71,109,120,126,127],msan:0,mscgen:[1,16],msd:[21,24,32,35],msf:90,msg:17,msvc:[7,20],mtot:40,mttk:125,mtx:[45,71,76,109],much:[1,3,8,9,19,20,24,68,69,111,119,121,125,126,127],mult:[116,121],multi:[1,20,71,81,98,119,120,124,125],multidir:[71,126],multilin:1,multilinear:24,multimer:[107,120],multipl:[0,1,3,8,9,13,15,16,17,20,24,25,26,29,46,49,51,56,59,68,71,72,81,97,98,107,113,117,118,120,125,126,127],multipli:[20,21,49,55,66,100,109,118,121,125],multiprot:120,mumax:40,mumber:125,must:[0,1,3,13,16,20,25,26,40,44,50,51,57,61,66,68,71,87,89,90,91,95,100,107,109,113,114,118,120,121,125,126,127],mutant:32,mutex:0,mutot:51,mutual:[75,120],mvacf:44,mwa:34,mxn:119,myclass:1,mylib:125,mymethod:1,n2t:115,nab:102,name:[0,1,3,5],namespac:[1,2,9],nanosecond:[29,48,121,125],nativ:[13,20,26,119,125,127],natom:[69,121],natur:[1,2,3,8,20,61,98,126],navig:[1,20],nbfgscorr:125,nbfunc:121,nbin:26,nbmax:[26,51],nbmin:[26,51],nbnxn:120,nbootstrap:113,nbox:55,nbsearch:15,nclust:31,nco:40,ncoord:125,ncpus:120,nd1:81,ndec:107,ndef:48,ndegre:40,ndf:31,ndiff:126,ndih:29,ndot:95,ndx:[23,25,27,28,30,31,32,33,34,35,36,37,38,40,41,42,43,44,46,47,48,52,53,54,56,57,58,59,60,61,62,63,65,66,68,69,70,71,72,73,74,75,77,79,80,81,83,84,85,87,88,89,90,91,92,94,95,96,97,98,101,102,103,104,105,106,107,108,109,110,111,112,118],ne2:81,nearest:[30,46,95,107,125],nearli:[1,20,69,119,125,127],necessari:[0,1,6,9,13,15,16,17,20,44,47,49,54,58,67,69,75,81,84,101,109,117,118,119,120,122,125,126,127],necessarili:[81,88],ned:7,need:[0,1,2,3,6,7,8,13,15,16,17,20,31,32,33,34,40,44,51,52,58,61,63,67,68,69,71,76,81,89,94,98,105,106,107,109,112,113,117,118,119,120,121,123,125,126,127],neg:[24,56,109,116,117,120,125,126],negat:[117,118],neglect:109,neglig:[20,120,125],neighbor:[30,71,81,113,120],neighborhood:118,neighborlist:125,neighbour:115,neither:[0,120],nemd:58,neon:20,net:[40,58,84,103],network:[20,127],neutral:[35,56,81],neutron:[21,118],never:[0,1,4,13,20,71,93,120,125],nevskip:23,newer:[0,9,16,20,43,127],newton:[0,125],newtonian:[21,125],nex:71,nexcl:115,next:[1,4,20,48,61,71,81,123,125,127],nframe:[23,47,78],nfs:121,ngrid:98,ngroup:[75,125],nh3:81,nhbdist:61,nice:[21,71],nicelevel:21,nine:121,ninja:[0,20],ninsert:53,ninterm:74,nitacc:61,niter:[30,125],nitrogen:61,nlevel:[30,31,38,40,41,50,65,70,88,89,98,110],nme:81,nmeig:[21,23,68,71],nmen:[21,76],nmol:[51,59,66],nmr3:89,nmr6:89,nmr:[29,89,121],nmrpdb:[23,27,32,107],nmtraj:21,nname:56,nnnice:114,no_format_check:17,noappend:71,noc:48,noda:61,noddcheck:127,node:[3,20,71,95,120,124,125,126],nodiv:102,noe:89,nois:[120,125],noisi:[44,58,71,82,120],nojump:[35,52,105,107],nolog:113,nomw:75,non:[1,2,3,19,20,28,29,34,36,37,53,61,71,78,81,87,89,95,102,104,107,109,113,117],nonbond:[67,127],none:[1,20,22,23,24,25,26,27,29,30,31,34,35,36,39,40,41,42,43,44,46,50,51,53,54,59,60,61,63,66,67,68,70,71,72,74,75,76,77,79,80,81,83,84,85,86,87,88,89,90,91,92,94,95,96,97,98,99,101,102,103,104,105,106,107,108,109,110,111,113,116,117,121,125],nonlinear:125,nonloc:127,nonorm:87,nonzero:[68,120,125],nopbc:118,nor:[0,1,4,120],norm:[40,42,46,76,87,97,105],normal:[0,13,20],normdo:44,normhisto:29,nose:[33,58,125],notabl:20,notat:[3,8],note:[0,1,2,3,4,9,13,15,17,19,20,23,25,26,29,33,34,36,42,43,44,45,48,51,53,58,61,63,68,71,75,79,81,85,87,90,94,97,98,102,104,107,109,110,113,117,118,119,120,121,125,127],noth:[1,2,6,13,15,20,81],notic:[1,117],notunepm:[125,127],now:[5,16,20,24,33,36,118,121,125],nparm:91,npme:[71,109,127],npoint:125,npstring:109,npt:[36,51,125],nrandom:30,nratio:125,nrelectron:36,nresnr:29,nrexcl:121,nsfactor:94,nshell:108,nskip:[31,113],nsmooth:39,nst:[30,125],nstart:125,nstcalcenergi:[125,127],nstcgsteep:125,nstcomm:125,nstdhdl:125,nstdisreout:125,nstenergi:[121,125,127],nstep:[33,71,109,121,125,126],nstexpand:125,nstfout:125,nstgbradii:125,nstlist:[71,119,120,125,126,127],nstlog:[121,125,127],nstorireout:125,nstpcoupl:[125,127],nsttcoupl:[125,127],nstvout:[111,125],nstxout:[121,125],ntemp:125,nth:125,ntmpi:[71,109,127],ntomp:[71,127],ntomp_pm:[71,127],ntop:41,ntpr:109,ntr:30,nuland:68,num:[61,70,77],num_expr1:117,num_expr2:117,num_expr:117,number:[3,20,23,24,25,26,27,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,47,48,50,51,53,54,55,56,57,58,59,60,61,62,65,66,68,69,70,71,72,74,75,76,77,78,79,80,81,82,83,84,87,88,89,91,92,93,94,95,96,97,98,100,102,104,105,106,107,108,109,110,111,1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genconf","gmx genion","gmx genrestr","gmx grompp","gmx gyrate","gmx h2order","gmx hbond","gmx helix","gmx helixorient","gmx help","gmx hydorder","gmx insert-molecules","gmx lie","gmx make_edi","gmx make_ndx","gmx mdmat","gmx mdrun","gmx mindist","gmx mk_angndx","gmx morph","gmx msd","gmx nmeig","gmx nmens","gmx nmtraj","gmx order","gmx pairdist","gmx pdb2gmx","gmx pme_error","gmx polystat","gmx potential","gmx principal","gmx rama","gmx rdf","gmx rms","gmx rmsdist","gmx rmsf","gmx rotacf","gmx rotmat","gmx saltbr","gmx sans","gmx sasa","gmx saxs","gmx select","gmx sham","gmx sigeps","gmx solvate","gmx sorient","gmx spatial","gmx spol","gmx tcaf","gmx traj","gmx trjcat","gmx trjconv","gmx trjorder","gmx tune_pme","gmx vanhove","gmx velacc","gmx view","gmx wham","gmx wheel","gmx x2top","gmx xpm2ps","Selection syntax and usage","Command-line reference","Non-bonded cut-off schemes","Environment Variables","File formats","Flow Chart","Getting started","User guide","Molecular dynamics parameters (.mdp options)","Useful mdrun features","Getting good performance from mdrun"],titleterms:{"class":1,"enum":1,"function":[1,120],"new":15,"public":1,"static":[6,20],acceler:[20,127],access:20,advanc:20,affect:0,after:20,algebra:20,algorithm:127,all:0,allow:7,anadock:22,anaeig:23,analysi:[6,21,23,113,118,120],analyz:[21,24,118],angl:[25,117],anneal:125,api:1,arbitrari:118,arithmet:117,aspect:20,atom:[117,118],atomnam:117,autocorrel:113,automat:17,background:[123,127],bar:26,base:117,basic:1,better:127,between:[21,23,118],binari:[13,20],bluegen:20,bond:[21,118,119,125],build:[0,1,6,15,16,20],bundl:27,cach:0,calcul:[23,125],chang:[16,20,118],chart:122,check:28,checker:3,chi:29,clang:6,classic:125,cluster:[20,30],clustsiz:31,cmake:[0,20],code:[0,1,2,8,9,16,17,18],codebas:9,com:125,command:[20,21,117,118],commit:17,common:[1,8],comparison:119,compil:[0,6,20],compon:20,comput:125,configur:20,confrm:32,construct:1,control:[1,120,125,126,127],convent:[8,118],convert:[21,33,118],coordin:[21,118],copyright:17,core:120,correct:20,coupl:125,covar:34,covari:[21,23,118],coverag:6,cppcheck:6,cpt:121,crai:20,cuda:20,current:35,cut:119,dat:121,data:13,debug:120,decomposit:127,defin:125,demand:6,densiti:36,densmap:37,densord:38,depend:3,der:125,descript:[21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116],detail:[3,121],develop:[5,9,16,19],dielectr:39,difficulti:20,dipol:40,direct:4,directori:1,dirti:20,disr:41,dist:117,distanc:[21,42,117,118],distribut:[21,118],dlg:121,do_dssp:43,document:[1,6,9,16,19],domain:127,download:18,doxygen:[1,9],dump:45,dyecoupl:46,dynam:[21,123,125],dyndom:47,edi:121,editconf:48,edr:121,electric:125,electrophysiolog:125,electrostat:[21,118,125],embed:126,eneconv:49,enemat:50,energi:[21,51,118,121,125],ensembl:125,environ:[120,123],equilibrium:125,error:113,evalu:117,ewald:125,exampl:[1,117,121,126,127],exchang:126,exclus:125,exist:1,expand:125,express:117,extend:117,external:0,fast:20,featur:[7,119,125,126],fftw:20,field:125,file:[1,3,8,13,21,118,121,123],filter:[17,52],find:[13,15,20,127],flag:0,flavor:1,flow:122,flowchart:123,format:[2,16,17,121],fortran:121,fourier:20,framework:15,free:125,freevolum:[53,118],from:[117,127],fujitsu:20,further:119,g96:121,g_bond:118,g_dist:118,g_sa:118,g_sgangl:118,gangl:[54,118],genbox:118,genconf:[55,118],gener:[1,16,21,118,125],genion:56,genrestr:57,get:[15,20,123,127],git:17,gmx:[21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,118],good:127,gpu:[20,127],graph:3,gro:[121,123],gromac:9,gromacs:[1,16,19,20,127],grompp:58,group:[1,125],guid:[5,9,20,124],guidelin:[1,2,4,8,14],gyrat:59,h2order:60,handl:118,hardwar:127,have:20,hbond:61,hdb:121,header:20,helix:62,helixori:63,help:[20,64],hook:17,how:[119,127],hydord:65,implicit:125,important:123,includ:4,include:3,index:123,indice:19,inform:[0,119,125,127],input:[121,123],insert:[66,118,125],insolidangl:117,instal:20,install:20,installat:20,instruct:20,intel:20,interact:[21,118],interfac:[21,118],introduct:20,issu:[3,13],issue:[25,29,36,44,45,48,49,55,56,60,61,84,100,102,112,115],itp:121,jenkin:6,keyword:117,kinet:[21,118],known:[13,25,29,36,44,45,48,49,55,56,60,61,84,100,102,112,115,127],langevin:125,languag:7,length:126,librari:[0,1,13,20],lie:67,limit:[117,127],line:[20,117,118],linear:20,link:[0,20],log:121,m2p:121,macro:1,make_edi:68,make_ndx:69,man:9,manag:[16,120],map:121,markup:1,mass:[21,118],materi:123,mdmat:70,mdp:[121,123,125],mdrun:[20,71,126,127],membran:126,merg:117,method:1,mindist:[72,117],minim:125,miss:10,mistak:1,mix:125,mk_angndx:73,mkl:20,mode:[21,118,126],modul:1,molecul:[66,118],molecular:[21,123,125],more:127,morph:74,mpi:20,msd:75,mtx:121,multi:126,name:[8,20,117,118],ndx:[121,123],neighbor:125,nmeig:76,nmen:77,nmr:125,nmtraj:78,node:127,non:[119,125],normal:[21,118],off:119,older:20,onli:20,opencl:[20,120,127],optim:117,option:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,118,125],order:[3,79],organ:9,organiz:9,other:[20,121],out:[121,127],output:[120,125],over:[21,118],overhead:127,overlap:23,overview:[0,9],page:[1,9],pairdist:[80,118],parallel:[20,113],paramet:[121,123,125],particl:125,pass:0,pdb2gmx:81,pdb:[121,123],pdbatomnam:117,pdbname:117,perform:[20,119,120,127],permut:117,phi:20,platform:20,plu:117,pme_error:82,polystat:83,portabl:20,posit:117,potenti:84,pre:[6,17],preprocess:125,prerequisit:20,pr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