http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
Cheers, Tsjerk On Thu, Jun 14, 2012 at 10:26 AM, Shima Arasteh <shima_arasteh2...@yahoo.com> wrote: > > Dear gmx friends, > > I put a protein in a simulation box filled of water molecules and entered > the mdrun command. After the simulation, I found the protein near one of the > edges of the box and not in center. What is the problem? Anyone may suggest > me? > Does it mean that the simulation is meaningless? > I expect the protein to stay in the center of box and goes unfold by passing > the time. > > Thanks in advance > Sincerely, > Shima > > > > -- > 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
