There is no box, so it can't move. There is a lattice specified by three lattice vectors defining the periodicity. These vectors are updated every step based on the pressure, if you use pressure coupling. You can specify the protein to have no net center of mass motion, by setting it as comm_grps in the .mdp file.
Cheers, Tsjerk On Fri, Jun 15, 2012 at 11:35 AM, Erik Marklund <er...@xray.bmc.uu.se> wrote: > Hi, > > All molecules diffuse. As such, proteins are expected to move about. > Preventing them form doing so is essentially non physical, so you'd need a > good and thought-through reason for doing so. > > Erik > > 15 jun 2012 kl. 10.27 skrev Shima Arasteh: > > Thanks. > I read that it doesn't matter if the protein moves and even protrudes the > box. It's OK, but there is a question here; why doesn't the box move rather > than the protein? > Is it possible for box to be defined every step?, then the protein would > stay in the center of the box. > > Sincerely, > Shima > ________________________________ > From: Mark Abraham <mark.abra...@anu.edu.au> > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Sent: Thursday, June 14, 2012 12:22 PM > Subject: Re: [gmx-users] protein near the edges of simulation box > > On 14/06/2012 5:47 PM, Shima Arasteh 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. > > See > http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions > > Mark > > -- > 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 > > -- > 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 > > > ----------------------------------------------- > Erik Marklund, PhD > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: +46 18 471 6688 fax: +46 18 511 755 > er...@xray.bmc.uu.se > http://www2.icm.uu.se/molbio/elflab/index.html > > > -- > 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
