Hi Yun, Make sure to remove jumps from the trajectory (trjconv -pbc nojump) before using g_mindist. Also visually check a frame that is reported to have closed contacts.
Hope it helps, Tsjerk On Nov 10, 2011 1:45 AM, "Yun Shi" <yunsh...@gmail.com> wrote: Sorry, I just found that even if I use a dodecahedron box with -d 1.2 nm, the min periodic image dist still dropped abruptly to 0.172 or something like this after around 35 ns or 30 ns (different trajectory with same topology). So I wonder if this is just inevitable and we should live with it? Thanks, Yun On Wed, Nov 9, 2011 at 4:18 PM, Yun Shi <yunsh...@gmail.com> wrote: > > Hello everyone, > > I am ... -- 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
-- 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
