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lypeptid:77,polystat:17,polyvec:79,pool:26,poor:0,poorli:123,pore:91,port:[16,67],portion:3,pos_expr:113,posexpr:113,posit:[3,17,32,33,38,41,49,50,52,53,54,56,62,64,67,71,73,76,77,78,83,86,91,93,97,98,99,103,106,109,112],position_restraint:53,positionr:117,posr:[53,77,121],posrefc:77,posscript:117,possibl:[0,1,3,7,9,11,13,16,26,31,35,54,80,88,93,98,102,103,105,109,113,114,116,117,121,122,123],post:[1,16,114],postiv:121,postma:119,postprocess:114,postscript:[17,33,39,66,84,108,110,112,114,117],postyp:113,pot:109,potenti:[4,17,26,44,47,64,67],potj:95,pow:95,power6:16,power7:16,power8:16,power:[17,20,36,37,40,95,114,121],pp_pme:[67,123],ppc:16,pqr:44,practial:121,practic:[16,67,96,120,121],pre:12,prec:[22,117],preced:[57,113,114,117],precis:[16,19,22,29,30,40,47,54,64,67,72,73,74,100,101,103,105,107,115,117,121],precondit:16,predat:1,predefin:[62,121],predetermin:2,predict:116,prefer:[0,1,4,7,16,109,117,123],prefix:[0,1,7,9,16,77,113,116],preliminari:[15,16,98],prepar:[9,26,114],preparatori:98,prepend:[103,113],preprocess:41,preprocessor:[7,54,117,121],prereleas:16,prerequisit:[0,15],prerequisite_softwar:16,prescrib:12,presenc:[6,24,123],present:[4,7,12,16,19,20,22,24,27,44,47,62,67,86,93,101,102,109,111,114,116,117,121,123],preserv:[4,48,54,67,77],preset:74,press:[2,16,67,113],pressur:[24,29,32,67,106,117,119],pretti:[16,98,123],prev:84,prevent:[13,16,116,122],previou:[16,36,53,67,84,105,109,114,116,121,122,123],previous:[3,16,67,103],prframe:90,primarili:[12,17,122],prime:121,primer:11,primit:[17,111,114],princ:44,princip:[17,19,20,21,44,55,79],principl:47,print:[0,3,9,11,13,17,18,20,21,22,24,25,27,33,37,40,41,47,49,54,56,58,64,67,72,79,93,99,104,109,111,114,115,116,117,119,121,123],printresnam:68,prior:[19,64,72,98,121],prioriti:[16,116],privat:[1,3],privileg:16,prob:94,probabl:[0,16,21,25,30,32,94,106,109,117,121],probe:[9,49,91,114,122],problem:[1,4,7,16,24,25,32,41,96,113,121,122,123],problemat:3,proce:[9,31,113],procedur:[16,20,35,54,88,101,103,121,122],process:[1,9,12,13],processor:[16,116,117,121,123],produc:[0,1,3,8,11,12,13,16,20,25,27,33,36,43,44,49,53,54,67,71,83,84,85,88,90,93,94,114,116,117,121,123],product:[0,16,19,36,59,72,87,94,99,121,123],profil:[0,32,34,109,121],program:[0,8,9],programcontextinterfac:9,programmat:9,progress:103,proj:19,project:[16,19,64,67],prompt:[19,47,64,77,113,114],promt:113,proper:[4,8,98,111,113,117,121],properli:[16,25,33,67,98,109,115,116,119],proport:[16,19,20,51,57,121],prot:91,protect:[0,1,113],protocol:117,proton:[77,114],prove:16,provid:[0,1,2,3,4,6,8,9,11,12,13,15,16,22,24,32,38,42,47,49,50,53,67,71,72,76,83,88,91,93,101,103,105,109,112,113,114,120,121,122,123],pseudo:[3,34,121],psi:[25,58,82],pthread:123,ptx:116,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],publicli:[1,3],publish:119,pull:[26,67,109,116],pullf:[67,105,109],pullx:[67,105,109],puls:[116,121,123],pure:[20,29,35],purpos:[1,3,6,9,43,59,94,116,121,123],push:[1,12,16,122],put:[0,1,2,3,4,7,44,64,96,103,117,121],pygment:16,pymol:[16,74],python:[0,2,3,12,13,16],qcorr:72,qmbasi:121,qmcharg:121,qmmethod:121,qmmm:121,qmmmscheme:121,qmmult:121,qstep:90,quad:36,quadro:16,quadruplet:21,quadrupol:36,qualifi:1,qualiti:[16,22,115,123],quant_corr:72,quantiti:[23,94,103,121,122,123],quantum:[47,72],quarter:123,quartet:50,quasi:[19,121],quasiharmon:[19,64],question:[1,15,16,17],queu:122,queue:122,quick:[4,11],quickli:1,quiet:[9,17,114],quieter:1,quit:[1,11,12,16,17,32],quot:[3,4,9,17,64,113,116],r_0:[42,106],r_i:55,race:0,rad:[25,111,122],radacc:64,radcon:64,radeon:123,radfix:64,radial:[17,23,33,75,83,114,121],radian:25,radii:[24,44,49,55,62,79,96,105,121],radiobutton:117,radiu:[17,42,44,49,51,55,57,58,59,62,64,79,91,96,104,114,121,122],radstep:64,rahman:[54,117,121],rai:[17,25,77,92,114],rainbow:112,rais:121,rama:[17,25],ramachandran:[17,25,114],raman:57,ramomega:25,ran:16,random:[12,17,19,20,26,49,51,52,62,67,73,78,90,109,114,117,121,122],randomli:[51,52,62,73,109,121],rang:[16,22,44,53,57,83,103,112,115,116,117,121,123],rank:[16,17,64,67,105,114,115,116,121,122,123],rapid:16,rare:[6,9,13],rasmol:[19,23,28,44,103,104,116],rate:[20,57,121],rather:[1,16,21,25,27,35,36,37,40,43,44,46,47,49,53,59,91,116,121],ratio:[17,22,48,114,121],rational:[1,3,7],ravg:47,raw:[26,61,114],rbin:[57,97,106],rcmax:36,rcon:[67,123],rcoulomb:[105,115,116,117,121],rdd:[67,123],rdf:17,rdf_cn:83,rdist:113,rdtscp:16,reach:[8,16,52,64,67,79,121,122],reaction:[31,35,36,109,115,121],read:[0,1,11,16,19,20,21,23,24,25,26,27,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,54,55,56,57,58,59,61,62,63,64,65,66,67,68,70,71,75,76,77,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,96,97,98,99,100,101,102,103,104,106,107,108,109,112,113,114,116,117],read_first_xtc:117,read_next_xtc:117,readabl:[0,7,17,41,114,117],reader:[1,7,117,119],readi:[16,117],readm:8,readxtc:117,real:[9,16,18,19,20,21,22,24,25,26,27,29,31,33,34,35,36,37,38,40,42,43,44,45,46,47,49,50,52,53,54,55,57,61,62,63,64,66,67,68,69,70,72,73,74,76,77,78,80,83,84,85,87,89,90,91,92,94,95,96,97,98,99,100,101,103,104,105,106,107,108,109,110,111,112,113,117,121,123],realli:[16,121],reason:[1,2,8,11,15,16,31,105,108,112,113,115,121],rebas:13,rebuild:11,rebuilt:11,recalcul:47,receiv:[16,67],recent:[16,67,115],receptor:63,recip:[40,107],reciproc:[67,78,105,121],recogn:[113,114,116],recognit:119,recombin:20,recommend:[1,16,49,51,52,54,72,103,121],recompil:16,record:[21,44,77,86,91,103,116,117],recov:43,rect:103,rectangular:[44,103,117,121],recurs:13,red:[112,117,123],redmin:[12,13],redo:121,reduc:[0,16,20,30,34,48,98,103,106,115,117,121],reduct:[116,121],ref:[11,30,54,76,83,88,103,109,117,121],refactor:[2,4],refat:99,refcoord:121,refdata:11,refer:[0,1,6,8,11,12,15,16,17,23,28,30,32,38,46,47,48,49,50,64,71,75,76,80,83,84,85,86,88,91,93,97,99,103,104,113],referenc:[1,7],refgroup:76,reflect:1,reform:57,reformat:[3,4,5,12],reformat_al:[3,12],refus:[13,16],regard:[57,117],region:[25,31,64,98,121],regist:[0,16],regress:[0,8,11,12],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],regressiontest_download:0,regressiontest_path:[0,16],regressiontests_md5sum:12,regressiontests_tarbal:12,regular:[67,103,113],reidel:119,reintroduc:114,reject:[64,121],rel:[1,4,9,16,20,22,24,32,44,49,59,77,103,113,121],relat:[0,1,3,5,8,9,11,15,16,20,64,71,115,116,117,119,121,122],relax:[32,35,116,121,122],releas:[0,1,12,39,116,123],relev:[1,8,11,12,15,16,75,115,121,122,123],reli:[6,9,16,22,103],reliabl:[16,31,103],reloc:[9,16],relocat:[0,5],relwithassert:0,relwithdebinfo:0,remain:[1,7,12,16,26,54,77,103,105,113,121,123],remd:102,remdih:111,rememb:[27,121],remot:67,remov:[0,1,3,13,16,20,27,29,31,32,44,45,48,53,54,67,71,77,88,96,101,102,106,108,111,114,115,117,121,122],renam:[2,3,4,7,16,65,67,114,116,121],render:74,renum:[54,77],renumb:[44,51,54,77,116],reorder:[26,77,104,116],repeat:[0,1,26,105,121,122],repeatedli:16,repetit:7,replac:[0,1,3,13,52,109,114,121],replex:[67,122],replic:12,replica:[67,121],report:[0,3,6,11,13,16,47,116,121],repositori:[0,2,5,6,8,13,16],repres:[1,20,44,59,83,91,109,121],represent:[3,34,64,103,110,116],reprod:[67,122],reproduc:[67,116,120],repuls:[95,121],request:[0,47,54,114,123],requir:[0,1,3,5,6,8,9,11,12,13,16,19,23,26,29,30,31,44,54,57,59,63,64,67,88,91,92,94,98,99,103,105,113,114,116,121,122,123],rerun:[17,67,105,114,116,121,122],res_cog:[38,49,50,76,83,91,93,113],res_com:[38,49,50,76,83,91,93,113,114],resarea:91,rescal:[117,121],rese:[67,122],research:17,resembl:[7,20],reserv:[7,113],reset:[0,105,121],resetstep:105,resid:[1,5,113],residu:[17,23,25,39,44,46,51,52,57,58,59,65,66,68,76,77,82,85,86,91,93,96,103,110,111,113,114,116,117,121],residuetyp:77,resindex:113,resiz:122,resnam:[89,93,113],resnr:[44,89,93,113,117],resolut:116,resolv:[9,16,25,54,77],resouc:15,resourc:[16,123],respect:[1,4,13,16,20,23,32,54,56,68,70,77,83,84,86,94,103,105,109,113,114,116,121,122,123],respertim:68,respons:[7,9,31,122],rest:[1,16,21,25,26,96,121,122],restart:[54,64,71,109,121],restr:37,restrain:[54,64,121],restraint:[17,37,41,47,53,54,77,114,116,121,122],restran:25,restrict:[16,96,109,113,121,123],restructuredtext:[8,12],result:[0,1,9,11,12,13,16,18,20,22,26,31,43,49,53,54,57,62,64,67,72,76,91,96,100,103,105,111,113,116,121,123],ret:[42,117],reus:121,reusabl:11,rev:[13,100],reveal:[3,4,9,16],revers:[20,121],revert:13,review:[2,12],rework:7,rewrit:1,rewritten:[9,114],rgb:[27,117],rgbhi:27,rgblo:27,rgbradii:121,rhf:121,rhist:42,rho:[84,100],rhombic:[44,103],rhosc:84,rid:[8,9],ridden:16,ride:116,right:[1,11],rigid:121,ring:77,rise:[58,59,121],risk:16,rkappa:42,rlist:[115,121],rlistlong:121,rmax:[33,83,97,99,105,106,114],rmcomm:71,rmdh:45,rmin:[44,52,97,99,105],rmpbc:[38,49,50,76,83,91,93],rmsd:[17,18,24,26,28,43,47,64,70,84,85,88,114,117],rmsdev:86,rmsdist:17,rmsdmir:84,rmsf:[17,19],rmsmean:85,rmsmin:26,rmsscale:85,rmvsbd:54,robust:[9,109],rolandschulz:13,roman:117,root2:112,root:[0,1,8,9,16,19,28,55,71,84,85,86,112,121],rot0:110,rot:[51,62,84,98,103],rotacf:17,rotam:[21,25],rotangl:[67,105],rotat:[17,19,31,36,43,44,51,59,62,67,73,74,77,84,87,88,98,101,105,108,110,114,117,121],rotmat:17,rotref:54,rotslab:[67,105],rottorqu:[67,105],rotxi:[88,103],rough:24,rougher:83,roughli:[0,16,49,115,121],round:[103,111,117],routin:[1,8,16,31,44,117,121],row:[44,112,117],rpath:9,rst:8,rt41c5:117,rtol:121,rtp:[77,111,116],rtpi:121,rtpre:77,rudimentari:0,run:[0,1,3,6,8,9],runav:[67,105],runavgdf:47,rundir:67,runtim:[16,29,116,121,123],rvdw:[44,105,115,116,117,121],rvec:117,ryckaert:[21,69],s_a:22,s_b:22,s_idealga:47,sadli:16,safe:[31,123],safeti:0,sai:[16,22,32],salt:[17,52,114,121],saltbr:17,saltconc:121,sam:[64,67,105],same:[0,1,3,4,6,7,8,9,11,12,13,16,18,19,20,22,26,28,30,36,38,39,44,47,50,52,57,59,67,76,77,83,93,94,97,99,100,101,103,105,109,111],sampl:[12,17,19,22,47,64,67,94,105,109,114],san:17,sander:[91,119],sandi:16,sanit:0,sasa:17,satisfi:16,satisfiex:113,save:[16,40,103,116,121],sax:17,scale:[20,32,33,36,44,62,64,72,83,84,85,96,101,105,106,107,108,112,115,116,117,121,122,123],scalefac:45,scalevdw:105,scan:4,scatter:[17,114],scd:75,scdist:99,scenario:[12,32,67],scf:116,scharf:91,schedul:16,scheek:64,scheme:[15,16,64,94],schlitter:19,scientif:123,scl:85,scoped_ptr:4,scount:[39,97],screen:[54,72,108],screw:[51,111],script:[0,1,2],scroll:16,scum:97,sd2:121,sdf:98,sdk:16,search:[0,8,9,16,41,67,76,77,114,116],second:[1,11,20,28,33,35,43,47,50,57,59,70,76,79,84,93,94,99,103,112,113,117,121,123],secondaccessor:1,secondari:[17,39,68,114,117,119],section:[0,1,3,8,10,13,16,24,52,113,114,116,122,123],secur:11,sed:4,see:[0,1,2,3,4,5,6,8,11,12,13,16,20,22,42,43,47,50,53,54,57,58,61,62,66,67,70,72,75,76,84,91,94,100,103,109,113,114,116,117,119,120,121,122,123],seed:[26,49,51,52,62,67,73,78,90,109,121,122],seek:[105,123],seem:121,seen:[68,113],segment:[30,98],segv:27,sel:[57,76,83],select:[0,1,11,16,17,19,21,26,28,33,37,38,44,45,46,47,49,50,57,61,64,65,67,70,72,73,74,75,76,77,82,83,84,89,91],selectioncollect:11,self:[1,78,121],selgroup:76,selrpo:[38,49,50,76,83,91,93,113],seltyp:[38,50,76,83,93,113,114],semi:4,semicolon:[16,113],semiisotrop:121,send:111,sens:[7,11,20,24,37,93,110,115,121],sensibl:16,sensic:91,sensit:[16,121],sent:67,sep:[89,103],separ:[0,1,2,3,4,7,8,11,12,16,19,20,21,25,26,27,28,36,39,46,50,54,61,67,68,76,77,89,94,103,105,112,113,114,116,117,121,122,123],separate_dhdl_fil:22,seper:121,sequenc:[16,58,110,117,121],sequenti:85,ser:85,seri:[16,22,49,122,123],seriou:[16,74,121,123],serv:[54,121],server:16,session:117,set:[0,1,2,3,4,5,6,8,9,11,12],setenv:39,setfoo:7,settim:[45,102],settl:27,setup:[12,13,16,65,109,115,116,117,121,123],seventh:121,sever:[0,2,9,12,13,16,23,25,26,45,62,64,97,102,105,109,113,116,117,118,121,123],sfactor:92,sgang1:61,sgang2:61,sgsl:75,shake:[27,121],sham:17,shamlog:94,shanno:121,shape:[19,32,40,48,83,103,121],share:[0,1,5,8],shared_ptr:0,shear:[100,121],sheet:117,shell:[0,9,12,16,57,96,98,104,113,116],shift:[23,25,31,32,54,64,68,103,105,115,121,123],ship:16,shortcom:16,shorter:[20,107,110],shortest:[44,83,104,114,121],shortli:122,should:[0,1,2,3,4,6,7,9,11,16,19,20,21,22,26,29,30,31,32,33,35,38,39,40,43,45,46,50,51,52,57,59,62,67,72,74,75,76,77,79,80,86,90,91,96,97,100,102,103,105,107,109,113,114,115,116,117,119,121,122,123],shouldn:121,show:[0,1,3,6,8,9,11,12,16,19,20,41,86,93,94,108,112,114,115,117],shown:[3,11,117],shrink:122,shuffl:[26,51],side:[0,3,8,16,31,32,44,64,80,117],sidechain:[25,59],sig56:44,sig:95,sigep:17,sigfac:95,sigint:116,sigma:[17,20,44,45,72,95,109,114,116,121],sign:[16,52,64,121],signal:[67,116],signifi:3,signific:[1,16,84,114,121,122],significantli:[0,1,16,44,76,114],sigterm:116,sigusr1:116,silenc:3,sim:[47,121],simd:[0,3],similar:[1,2,3,9,13,16,29,44,84,109,121,122],similarli:[1,16,24,50,67,81,114,122],simpl:[1,3,11,16,77,82,93,95,96,109,117,121,123],simpleaccessor:1,simplest:[16,115],simpli:[1,6,9,32,47,51,54,58,74,96,98,102,105,113,114,117,121],simplic:[16,116],simul:[0,16],simultan:[46,103,112,116,121],sin:[21,94],sinc:[0,1,3,8,12,16,19,20,29,31,32,39,48,49,53,64,73,74,77,87,88,90,96,98,102,116,121,122],sine:100,singl:[0,1,2,3,7,8,15,16,19,25,26,36,38,42,47,49,50,53,57,64,67,76,77,83,91,93,94,103,112,113,114,115,120,121,122],singular:121,sinh:100,site:[14,16,24,54,72,77,96,115,121],situat:[1,121,122],six:[73,74,123],size:[0,16,17,20,26,27,32,33,44,49,55,59,62,67,83,84,93,96,98,103,112,113,114,115,116,117,119,121,122,123],skip2:84,skip:[0,3,19,20,26,27,36,46,47,84,88,94,103,112,116,117,123],sksl:75,slab:[36,121],slice:[32,36,55,56,75,80],slight:121,slightli:[77,113,116,121,122],slope:64,slow:[11,36,64,77,106,116,121],slower:[16,113,115,121],slowli:[15,16,123],small:[17,25,26,32,34,51,62,83,96,103,113,114,115,116,121,122],smaller:[16,24,58,64,67,76,105,114,117,121,122],smallest:[26,66,104,123],smart:[16,102],smear:32,smi:16,smooth:[17,26,35,48,103,109,112,114,116,121],smoothli:[26,121],snor:97,soc:119,socket:123,soft:[116,121],softwar:[0,16,117,119,123],sol:[46,113,117,121],sole:[0,54,116],solut:[1,16,17,44,62,96,97,98,99,114,119],solv:[6,9,116,121],solvat:[17,91],solvent:[17,29,39,52,57,63,91,96,97,98,99,114,115,116,119],solver:[44,121],some:[0,1,2,3,4,5,6,7,8,9,11,12,13,15],someclass:1,someon:4,someth:[1,12,102,123],sometim:[16,77,119,121,123],somewhat:[1,105,111,114,121],somewher:[11,115],soon:[113,116],sophist:[96,109],sord:97,sori:97,sorient:17,sorter:[3,4,12,13],source_md5sum:[0,12],source_tarbal:12,space:[2,16,21,22,25,33,51,62,64,78,90,98,103,105,106,109,114,116,117,121,123],span:[31,87,113,121],sparc64:16,sparc64_hpc_ac:16,sparc64viiifx:16,sparc:16,spatial:[17,34],spc216:96,spc:[36,77,96,117],spce:77,speak:7,specialist:16,specif:0,specifi:[0,1,3,12,13,16,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112],speckl:98,spect:[34,61],spectra:[17,90,107,114],spectroscopi:57,spectrum:[40,72,107],speed:[1,16,113,114,121],sphere:[49,50,91,117,121],spheric:[80,121],sphinx:[0,8,12,16],sphnorm:50,spline:116,split:[2,5,15,19,22,55,65,68,71,78,79,84,91,99,103,114,121,123],spme:[78,121],spoel:[25,109,121],spol:17,spontan:64,spread:[117,123],spring:64,spuriou:121,sqframe:90,sqrt:[19,20,44,55,58,72,100,106],squar:[16,17,19,20,26,28,30,31,40,47,55,70,71,79,84,85,86,88,114,117,121],src:[0,1,4],srun:16,ssdump:[25,39],sse2:[16,116],sse4:[16,116],sss:39,stabl:[98,121],stack:[0,1,51,96],stage:[16,122],stai:[13,103,115,121],stamp:102,stand:[46,57,93,117],standard:[0,1,4,7,8,9,16,20,22,25,38,40,41,49,64,72,77,85,86,91,103,108,109,116,117,121,123],start:[1,3,4,7,8],startq:[90,92],startup:[17,116],stat:[9,121],state:[7,17,22,24,29,40,41,44,46,47,52,67,77,105,114,116,117,121],state_prev:67,statement:[0,2,3,4,54,117],statist:[18,22,25,31,38,45,47,71,105,109,116,121],statu:[11,16],std:[0,1],stddev:20,stderr:[3,67,121,123],stdev:22,stdin:11,stdio:4,stdout:[33,123],stead:117,steep:121,steepest:121,steer:16,stem:78,step:[16,26,29,36,37,43,47,48,54,58,64,67,90,98,103,105,114,115,116,117,118,119,121,122,123],stepsiz:64,still:[1,3,9,12,13,16,27,32,54,83,98,113,114,115,121,122,123],stimul:64,sto:121,stochast:[67,121],stop:[16,20,45,57,67,109,116,117,121],store:[3,11,16,20,37,44,47,64,66,67,71,102,104,106,113,117,121],straight:[31,47,71,79],straightforward:[11,16],strain:121,strang:81,strategi:121,stream:123,strength:[64,121],stricter:[3,12],strictli:[7,113],stride:[113,123],string:[0,11,16,22,24,32,34,36,39,44,52,56,63,64,67,74,77,80,103,105,110,111,113,117,123],stringtest:11,stringutil:11,strip:[0,77],strong:[16,117,123],strongli:[16,20,115],structur:[1,9],struggl:16,stryer:119,stuck:121,studi:121,studio:[0,9,16],stuff:123,style:[1,3,4,5,6],stylesheet:11,sub:[103,112],subav:20,subclass:1,subdirectori:[1,3,8,11,12,16,22,77],subexpress:113,subgroup:[17,114],subinterv:93,subject:[12,13,15,16,32,121],subpag:1,subroutin:121,subsequ:[1,9,21,22,77,96,98,102,103,117],subset:[0,8,15,16,29,91,103,105,122,123],subspac:[19,64,73],substanti:[32,40,109],subsystem:121,subtitl:22,subtleti:1,subtop:113,subtract:[20,36,47,72,77,99,113,115,121],subtrajectori:103,succe:[0,12],succeed:116,success:[0,9,117],successfulli:[0,16],sudo:16,suffic:[105,121],suffici:[1,40,52,67,98,105,109,119,121],suffix:[0,1,7,13,16,122],suggest:[16,57,67,98,103,113],suit:[0,11,12,16],suitabl:[0,3,8,9,16,53,63,76,114,117,123],sulfat:52,sulfoxid:119,sum:[0,20,24,30,33,46,47,49,62,80,88,96,97,103,105,116,121],sum_i:[55,58],sum_k:121,sumh:85,summar:24,summari:[6,11,116],summat:[16,31,121],superimpos:[26,28],superposit:[28,84,86],suppli:[19,20,24,25,26,29,33,46,54,63,65,84,85,86,94,103,111,112,114,115,117,121,122],support:[0,1,3,8,9,11],suppos:119,sure:[16,20,48,67,71,77,86,98,100,107,121,122,123],surf:83,surfac:[17,32,34,39,83,91,94,98,114,116,121],surround:31,suspect:67,suspend:122,swap:[67,105,121],swapion:[67,105],swift:39,sym:109,symbol:[0,2,7,9,114],symm:32,symmetr:[16,32,109,121],sync:5,synchron:11,synonym:113,syntact:113,syntax:[3,39,93],systemat:[105,122],szonli:75,t_exampl:1,t_struct:1,t_sym:121,tab:[1,2,8,109],table_na_cl:121,table_na_na:121,tableb:[67,105],tablep:[67,105,121],tabletf:[67,105,121],tabul:[67,109,115,116,121,123],tag:[1,3],tail:[17,35,43,75,114],take:[1,11,16,22,26,27,32,36,43,54,56,62,64,68,72,80,98,105,114,115,116,121,122,123],taken:[16,19,20,25,30,31,33,45,52,64,73,80,84,85,102,103,105,111,112,121],tangenti:34,tape:103,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],tarbal:[0,12,16],targer:0,task:[0,1,6,8,13,16,114,123],tau1:35,tau2:35,tau:[25,64,100,109,117,121],tau_1:20,tau_2:20,tavg:34,tblock:[34,61],tcaf:17,tcaf_al:100,tcaf_cub:100,tcaf_fit:100,tcoupl:[117,121],team:[2,16],techic:[1,8],technic:[6,15,16,113],techniqu:[109,123],tee:16,tell:[11,16,105],temp:[19,20,22,27,31,36,46,47,57,73,74,101,109,116,121],temper:121,temperatur:[17,19,20,22,24,27,29,31,36,40,46,47,49,57,64,67,72,73,74,86,94,101,109,114,115,116,117,119],templat:8,temporari:[11,105],t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system overview","Using Doxygen","Guidelines for code formatting","Source tree checker scripts","Guidelines for #include directives","Developer guide","Understanding Jenkins builds","Naming conventions","Codebase overview","Relocatable binaries","Style guidelines","Unit testing","Development-time tools","Automatic source code formatting","Downloads","Welcome to the GROMACS documentation!","Installation guide","molecular dynamics simulation suite","gmx anadock","gmx anaeig","gmx analyze","gmx angle","gmx bar","gmx bundle","gmx check","gmx chi","gmx cluster","gmx clustsize","gmx confrms","gmx convert-tpr","gmx covar","gmx current","gmx density","gmx densmap","gmx densorder","gmx dielectric","gmx dipoles","gmx disre","gmx distance","gmx do_dssp","gmx dos","gmx dump","gmx dyecoupl","gmx dyndom","gmx editconf","gmx eneconv","gmx enemat","gmx energy","gmx filter","gmx freevolume","gmx gangle","gmx 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 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