Hi, trjconv -s topol.tpr -f traj -pbc mol -o traj_modified select '0' for the entire system
You can try using either 'mol' or 'nojump' depending on your visualization needs. cheers, Tarak On Wed, Jan 29, 2014 at 3:39 PM, Atila Petrosian <atila.petros...@gmail.com>wrote: > Dear Gromacs users > > I did simulation of a system containing protein and cnt using gromacs > 4.5.6. > > When I see trajectory by VMD, in some frames, protein atoms exit one side > of box > and enter opposite side of box (pbc problem). I know I should use -pbc > option of > trjconv tool. But I do not know exactly which of none, mol, res, atom, > nojump, > cluster or whole is appropriate for me. The below link shows one frame of > trajectory: > > https://www.dropbox.com/s/vur8fh1apvp79lm/pbc%20problem.bmp > > Any help will highly appreciated > -- > 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.