you can use trjconv -pbc nojump to take care of that.
On 10/8/09, Pan Wu <pan...@duke.edu> wrote: > Hi Gromacs users, I am new to Gromacs, and now setting up one very simple > system to test Gromacs+Martini. (one protein with solvent surrounded) > When I run the MD and saw the trajectory, the protein seems go around > randomly, and across the box size. Because Periodic Boundary Condition, it > will come back from the other side. But I don't know *whether the across box > size movement will actually cause some problem about protein structure or > dynamics*? > > In my mdout.mdp file, I can see: > comm-mode = Linear > nstcomm = 1 > comm-grps = (default, should be system) > > Thank you in advance! > > Sincerely > Pan > > > > -- > Sincerely > ================================= > Pan Wu > Graduate Student in Department of Chemistry > Duke University > 124 Science Drive > 5301 French Family Science Center > Durham, NC 27708 > Phone: (919) 660-1583 > ================================= > _______________________________________________ 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
