Hi Jaowei Tang, Better use a .pdb or .gro file. Maybe the starting structure (obtained after running pdb2gmx)? By the way, if you removed the jumps over the boundary (you don't really want to remove periodicity :p) you must already have a proper structure. Or you can then extract the first frame from the trajectory and use that as the starting point.
Tsjerk On 10/4/07, tangxuan <[EMAIL PROTECTED]> wrote: > > Dear all, > I am try to use g_rms to a protein, but its start structure in the > simulation is not in one box. I removed the periodicity for the xtc file > by trjconv, but do not know how to remove the periodicity in the tpr > file. Could you give me some suggestions? > > Thank you. > > Jiaowei Tang > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623
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