Hi Saba, You can use g_mdmat or run g_rmsdist for different time windows. It's also a good idea to have a look at all the analysis tools and think of how they may suit your purpose.
Cheers, Tsjerk On Thu, Dec 1, 2011 at 5:43 AM, Saba Ferdous <saba.bsbi...@iiu.edu.pk> wrote: > Dear Sir, > I am studying a protein complex. I have perforemed 10ns simulations. I saved > snapshots every10ps. sp all snap shopts I got were 1000. > Now I want to analyse them with respect to interactions. I want to check the > binding surfaces and binding points which come closer and incontact during > simulations. Can you devise me a way to perform such kind of analysis. > Further more I am interested to know the binding energies as well. What sort > of other analysis can be done on this complex. > > -- > Saba Ferdous > Research Scholar (M. Phil) > National Center for Bioinformatics > Quaid-e-Azam University, Islamabad > Pakistan > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
