On Tue, Nov 24, 2009 at 1:09 PM, Omer Markovitch <omer...@gmail.com> wrote: > On Fri, Nov 20, 2009 at 01:32, Chih-Ying Lin <chihying2...@gmail.com> wrote: >> >> So, how can I remove the periodic boundary condition to get the truly >> movement of the atoms between the two time steps ? > > Removing PBC and placing atoms back into their "true" location is easy. In > general, if an atom has moved more than half of the box between two > consecutive timesteps then it has "jumped" over the box. > You can see for example eq. 19 & 20 in doi:10.1063/1.2968608 . > --Omer.
Hi, Removing periodicity from the trajectory can be done after simulation using g_traj with the "-nojump" option. Best, Lukasz -- Lukasz Cwiklik http://cwiklik.wordpress.com -- 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
