Hi Mustafa, Check the section on periodic boundary conditions in the manual. Also be sure to use 'show cell' in Pymol to display the triclinic unit cell. That will show you the differences. Besides that, do a direct comparison of the lines encoding the boxes; either the last line of a .gro fil, or the line starting with 'CRYST1' in a.pdb file.
Cheers, Tsjerk On Thu, Nov 4, 2010 at 1:23 AM, mustafa bilsel <mfbil...@gmail.com> wrote: > Hi, > when I choose different box types and draw them by Pymol, I see no visual > difference between them. At least cubic must be different from the others. > > What is the reason for this? > > best wishes > > -- > gmx-users mailing list gmx-us...@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