Hi, How about using g_dist and using an index file?!
Cheers Mohsen On Mon, Mar 23, 2015 at 6:50 PM, leila salimi <leilasal...@gmail.com> wrote: > Dear all, > > I have a question regarding to analyse the trajectory that I have. I am > studying the interaction of peptide at interfaces, e.g Oxygen of > carboxylate group of side chains with Cations at the interface! > I would like to calculate the distance between Oxygen of carboxylate group > of side chains and specific ions of solid at the interface! I used gmx rms > but I think I did wrong calculation. > > Could you suggest me which tool can give the overview of distance > fluctuation between two group of atoms? > > Regards, > Leila > -- > 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. > -- 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.
