Hi, Average structures are typically unphysical and rarely meaningful. Consider for instance the average structure of a spinning methyl group. Representative structures can be produced by clustering the frames in a trajectory and selecting the cluster centroids. See g_cluster.
Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Associate Department of Chemistry Physical & Theoretical Chemistry Laboratory University of Oxford South Parks Road Oxford OX1 3QZ On 24 Sep 2014, at 08:38, Mahboobeh Eslami <mahboobeh.esl...@yahoo.com> wrote: > Hi GMX users > what command should I use to obtain the average structure in pdb format for > two nanosecond of the end of simulation.Thank you sincerely for your help > -- > 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.
