Dear All, 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(for calculation of preferential interaction coefficient) I have a total of 18 urea molecules in my system. I have 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 molecules. But when I add -com option, all of the numbers decrease to 0 or 1. The problem persists even on increasing the no. of urea molecules to 40 or 80. So is it wrong to add -com option? Considering we're already specifying -da as 0? Yours sincerely, Apramita Chand -- 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.
