Hi, That doesn't necessarily "fix" the "problem". Which position of the protein is taken as a reference depends on the position of the first atom. Gromacs wants to have the first atom of a molecule in the rectangular unit cell at the origin. Even if you set comm removal for the group, the initial orientation and/or conformational changes may cause the first atom to jump over the boundaries.
Whatever the case, everyone doing MD simulations should be aware of periodic boundary conditions. There is no "outside of the box". Tsjerk On Fri, Jun 27, 2008 at 12:58 PM, Vitaly Chaban <[EMAIL PROTECTED]> wrote: >> am new to Gromacs. I tried a 10 ps simulation with a protein and after the >> run, the protein came out of the box.. is it good or bad? > Its terrible. If it runs away you'll never have a new such frolicsome > protein... ;) > >> How can I keep the protein in the box? > Just fix it. In .mdp file write comm-grps = _YOUR_PROTEIN_GROUP_ > > -- > Vitaly V. Chaban > School of Chemistry > National University of Kharkiv > Svobody sq.,4, Kharkiv 61077, Ukraine > email: [EMAIL PROTECTED] > skype: vvchaban > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > 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 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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
