I think Bhanu was embarrassed that one part of his protein was from one side and the remainder was from another. Of course, there cannot be a state 'outside' in reality.
TW> Whatever the case, everyone doing MD simulations should be aware of TW> periodic boundary conditions. There is no "outside of the box". TW> 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
