Hi Sameer, There is a quick and easy way to visualize hydrogen bonds. Convert your traj.trr file to .gro and open it in VMD software. You can then manipulate VMD options to show hydrogen bonds.
Dan On Sun, Aug 6, 2017 at 10:57 AM, Sameer Edirisinghe <noot...@gmail.com> wrote: > Dear all, > > I have done 200ns simulation for my polymeric system and I want to map all > existing nonbonded interactions (i.e. H bonds) in my system over the time. > Can anyone suggest me a method for this? > > > Regards > Bhagya karunarathna > -- > 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.
