Dear user, Tanks for your attention ,I read about trjconv,but I want to know is it necessary to back to the exact fram befor molecule split happens and then center the molecule by trjconv command? The other point,if you attention to my value”edit conf d=0.9 and during MD rvdw=1..4” is it broke the rule of periodic boundary condition or not? tanks
________________________________ From: Tsjerk Wassenaar <tsje...@gmail.com> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Fri, April 1, 2011 1:29:19 PM Subject: Re: [gmx-users] FW: protein split over boundary http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions -TAW On Fri, Apr 1, 2011 at 10:53 AM, anahita <ana_j0...@yahoo.com> wrote: > > > > > From: anahita [mailto:ana_j0...@yahoo.com] > Sent: Friday, April 01, 2011 1:13 PM > To: 'gmx-users-requ...@gromacs.org' > Subject: protein split over boundary > > > > Dear user, > > Hello, I appreciate if somebody help me. During the simulation of my protein > I didn’t get any error but after 1ns of MD > > my molecule was split over boundary in cubic box. it means some part of it > enter the other side of the box. > > At first,For decreasing the cost of simulation, in “editconf” command I set > the number “d” on 0.9 to decease the box size. I want to mention that > during the calculation my rvdw is 1.4. > > I want to know instead of problem of visualization, the other things is > fine? > > Best regards. > > A. johari > > -- > 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
-- 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
