With reference to my earlier message, I have also tried the g_trjorder command giving reference group as Backbone.
When I give the command, g_trjorder -f 100ns_nc_72um2.xtc -s md.tpr -nshell nshell_urea.xvg -r 0.45 -da 0 I am getting reasonable no.of urea molecules like 6,8,9,etc. Same goes for water moelcules. But when I add -com option, all of the numebrs decrease to 0 or 1. So is it wrong to add -com option? Considering we're already specifying -da as 0? Yours sincerely, Apramita Chand From: Apramita Chand <apramita.ch...@gmail.com> To: gmx-us...@gromacs.org Subject: [gmx-users] Doubts regarding g_select Message-ID: <ca+gtzozrewmzjhkh4tmpwha12wqr5ob0y_bu_w8fh16oqd3...@mail.gmail.com> Content-Type: text/plain; charset="UTF-8" Dear All, I am confused between different commands and their outputs for g_select. I want to choose a cutoff of 0.45nm and want to calculate the no. of urea molecules within 0.45 as well as beyond 0.45nm of the peptide backbone. I have a total of 18 urea molecules in my system One of the commands: g_select -select ' resname UREA and within 0.45 of group Backbone' -f 100nc_entire.xtc -s md.tpr -os size_within0.45_urea_backbone.xvg -oi index_within0.45_urea_backbone.dat -oc cfrac_urea_within0.45_backbone.xvg -seltype mol_com gives 6,5,4,3...etc urea molecules in the size.xvg file which seems to be correct But if I give the same command by changing it to g_select -select 'rdist=res_com distance from com of group Backbone; resname UREA and rdist<=0.45' I get 0 or 1 urea molecule for every time frame. Again, I want to generate no.of urea molecules beyond 0.45, Giving, g_select -select 'rdist=res_com distance from com of group Backbone; resname UREA and rdist<=0.45' I get all 18 urea molecules in the above 0.45 regime That is confusing! I think the first command that specified within 0.45 nm is correct for my system and I would like a similar command that can specify beyond 0.45nm. This problem persists even when I increase urea molecules to 40 or 80. THere's just 1 molecule below 0.45nm and all of the others above 0.45nm. But the hydrogen bond numbers show increasing no. of hydrogen bonds between peptide-urea (increases upto 6-9) . What could be going wrong? Any suggestions regarding this problem? Yours sincerely, Apramita -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.