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searchindex.js
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Search.setIndex({docnames:["index","method","settings","workflow","xml_structure"],envversion:{"sphinx.domains.c":1,"sphinx.domains.changeset":1,"sphinx.domains.cpp":1,"sphinx.domains.javascript":1,"sphinx.domains.math":1,"sphinx.domains.python":1,"sphinx.domains.rst":1,"sphinx.domains.std":1,"sphinx.ext.todo":1,sphinx:54},filenames:["index.rst","method.rst","settings.rst","workflow.rst","xml_structure.rst"],objects:{},objnames:{},objtypes:{},terms:{"0001_12345":3,"6b00595":0,"828_deg1_a1":2,"828_deg1_a2":2,"828_deg2":2,"case":2,"import":2,"new":4,"public":1,For:4,Nies:0,The:[1,2,3,4],There:2,aa_topol:3,about:4,abov:2,account:4,acs:0,activ:[2,4],active_sit:[2,4],adapt:0,add:[2,4],adjust:4,after:[2,4],allow:0,alpha:3,alreadi:4,angl:[2,4],angle_ch2:2,angle_ch3:2,anyth:4,appropri:2,assign:4,atom:[2,4],atom_nam:4,atomist:[0,2,3,4],attach:3,attribut:[2,4],avail:3,backamp:2,backmap:[0,4],baker:0,base:[2,4],bead:[2,4],below:2,better:1,bibtex:0,bisphenol:2,block:2,bond:[2,4],built:[2,4],c10:2,c11:2,c12:2,calcul:4,can:[2,3,4],carbon:4,cg_bead:4,cg_bond:2,cg_conf:[2,3],cg_configur:4,cg_molecul:4,cg_topol:2,chain_nam:4,charact:[2,4],charg:[2,4],charge_map:4,chemic:[0,2],cite:0,clean:3,coars:[0,2,4],code:3,comment:4,compon:2,comput:0,concept:2,conf:3,configur:[0,3,4],connect:[2,4],contain:4,containst:3,content:4,convert:4,coord:3,coordin:[0,2,3,4],correspond:2,could:2,creat:[2,4],cross:4,current:[2,4],declar:[2,4],defin:[2,4],definigin:2,definit:4,degre:[2,4],denot:2,depend:2,describ:[1,2,3,4],descript:[0,2],detail:1,diamin:2,differ:[2,4],diglycidyl:2,dihedr:[2,4],directli:4,directori:3,divid:3,document:2,dod:2,dodecan:[0,3],dodecane_set:3,dodecane_singl:[2,3],doe:4,doi:0,dot:4,doubl:4,dure:2,each:2,either:2,element:[2,4],end:3,entri:4,epo:2,epon:2,epoxi:2,equilibr:2,equilibrate_charg:[2,4],eric:0,ether:2,everi:[2,4],exampl:[2,3],exclud:2,exclus:[2,4],exclusion_at:4,exclusion_cg:4,exclusion_hyb_topol:3,exclusion_list:3,exist:4,explain:2,explicitli:2,express:4,file:[0,3],first:2,flow:1,follow:2,forcefield:2,format:[2,4],found:2,fragment:[2,4],from:[0,2,3,4],full:2,fulli:1,further:2,gener:[0,4],get:3,giovanni:0,given:4,global:4,grain:[0,2,4],gro:[2,3,4],gromac:[2,4],h23:2,h24:2,h25:2,has:[2,4],have:[2,4],here:[0,1,2,4],how:2,http:2,hyb_conf:[2,3],hyb_topol:[2,3],hyb_topolog:3,hybrid:[2,3,4],hybrid_configur:4,hybrid_topolog:4,hybrid_topologoi:4,ident:[2,4],illustr:[1,2],in_top:3,includ:[2,4],inform:[2,3],inject:4,input:[2,3,4],instanc:4,instead:4,interact:[2,4],isophron:2,itp:2,jakub:0,jctc:0,journal:0,keep:4,know:4,krajniak:0,label:4,labtool:3,lammp:4,level:2,like:2,line:4,link:2,list:[2,3,4],make:[2,4],manual:2,map:[0,2,3],max_bond:4,maximum:4,method:0,mind:4,molecul:[2,3,4],molecule_degre:[2,4],molecule_typ:[2,4],multipl:2,name:[2,4],need:4,network:0,neutral:4,next:2,non:[2,4],normal:4,notat:4,number:[2,4],numer:4,one:[2,4],onli:[1,2,4],oplsaa:2,option:[2,3,4],org:2,origin:2,other:[2,4],out_top:3,output:[2,4],packag:4,pair:4,pandiyan:0,param:4,paramet:4,part:[3,4],partial:[2,4],particl:[2,4],particla:2,particular:4,per:[2,4],pleas:0,polym:0,prepar:3,prepare_fil:3,present:0,principl:1,procedur:3,produc:3,purpos:0,put:[2,4],reaction:2,reactiv:2,reduc:4,refer:2,remark:4,remov:4,remove_cross:3,reorder_topolog:3,replac:2,repres:[2,4],represent:0,residu:4,resolut:0,revers:[0,2,3],root:4,rule:2,run:3,samaei:0,same:[2,4],section:[2,4],see:2,select:2,separ:[2,4],set:[0,3],settings_network:2,share:2,should:4,shown:2,sim0confout_final_aa_0:3,sim0topol_aa_0:3,similar:4,similarli:2,simpl:2,site:[2,4],sketch:1,sourc:[2,3],source_coordin:4,source_fil:2,source_topolog:4,src:3,star:2,start_backmap:3,step:[2,3],still:3,store:[2,4],structur:[2,4],sudharsan:0,support:[2,4],surround:2,system:[2,4],tag:2,take:4,taken:[2,4],theori:0,therefor:4,thi:[0,2,4],three:2,tool:[0,3],top:[2,3,4],topol:2,topolog:[2,3,4],transform:0,tree:4,two:[2,3],type:[2,4],typeid:4,unit:2,usag:3,use:2,used:[0,2,4],useful:4,user:4,using:[2,4],usr:2,valu:4,vari:2,veri:2,votca:2,weight:2,well:3,what:2,when:[2,4],whenev:4,where:2,which:[2,3,4],whole:[2,3,4],withing:4,work:1,workflow:0,www:2,xml:[0,2,3],you:[0,3,4],your:[0,4]},titles:["Documentation of bakery","Method","Configuration file","Workflow","XML settings file"],titleterms:{backmap:2,bakeri:0,cg_bead:2,cg_configur:2,cg_molecul:2,charge_map:2,configur:2,document:0,dodecan:2,file:[2,4],hybrid_configur:2,hybrid_topolog:2,method:1,network:2,set:[2,4],source_coordin:2,source_topolog:2,workflow:3,xml:4}})