> Message: 5 > Date: Tue, 29 Jun 2010 11:54:12 +0330 > From: leila karami <karami.lei...@gmail.com> > Subject: [gmx-users] g_msd and diffusion coefficent > To: gmx-users@gromacs.org > Message-ID: > <aanlktinlxdcdfo3ytlz_zcy-ppgr8b6jnwhc3fc7t...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Vitaly Chaban > > I know using index file but gromacs say : select only 1 group. what is this > group ? protein? or DNA?
It is not clear what exactly you want. To observe as one molecule moves in relation to another one? If this would have been my task, I would introduce some specific function of the distance between them vs time. Is it not easier just to calculate two diffusion constants corresponding to your particles of interest? Is it equilibrium MD that you perform? Vitaly -- 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/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/mailing_lists/users.php
