Ok..Thank you.. I'll extend my simulation upto 50 ns.
Thanks, Neha On Tue, Dec 19, 2017 at 12:44 PM, Nikhil Maroli <scinik...@gmail.com> wrote: > After MD simulation of protein-ligand complex for 5ns, can we view protein > folding? > > mostly, NO > > Search what time range 'protein folding' is happening. > > How to do it? > > I want to ascertain if there is any conformation change in protein where > the ligand binds. Is it possible? > > > You might want to do PCA, RMSD and DSSP > > We observe hydrogen bonds through molecular docking. Hence, I want to make > observation through MD simulation which is not obtained through docking. > > > gmx hbond > > Can someone help me regarding this? > > > i really wondering what is possible in 5 ns simulation time, you may > try to extend it up to 100 ns or atleast a 50 ns. > > Thank you very much in advance. > -- > 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.