Hi, You use a tool like gmx select to select all those atoms. Have a look at its help and examples.
Mark On Wed, 26 Jul 2017 20:00 Dilip H N <cy16f01.di...@nitk.edu.in> wrote: > yes thn how can i index the groups (say i want to calculate hbond b/w NH of > glycine and O of water)... > with commands... > > > > <https://mailtrack.io/> Sent with Mailtrack > < > https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.di...@nitk.edu.in&idSignature=22 > > > > On Wed, Jul 26, 2017 at 10:56 PM, Erik Marklund <erik.markl...@kemi.uu.se> > wrote: > > > > > > > On 26 Jul 2017, at 19:04, Dilip H N <cy16f01.di...@nitk.edu.in<mailto: > > cy16f01.di...@nitk.edu.in>> wrote: > > > > but i dont have any OH or NH groups in glycine,water mixture... > > > > Your water is packed with OH, and glycine has both NH and OH. > > > > Kind regards, > > Erik > > -- > > 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. > > > > > > -- > With Best Regards, > > DILIP.H.N > Ph.D Student > -- > 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.
