Hi, Indeed, it's the 'box-gets-lost-bug'. It happens with the tutorial because it was written for an earlier gromacs version. There's an updated one for 4.5.5 at http://md.chem.rug.nl/~mdcourse/molmod2012/
Although I'll check again if that bug may still cause problems... If you stick to .gro format for structures, you're always fine. Only if you want to use pymol or so, you need to convert it to .pdb. Cheers, Tsjerk On Fri, Jul 6, 2012 at 6:38 AM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > Hi, > > Indeede, it's the 'box-gets-lost-bug'. It happens with the tutorial because > it was written for an earlier gromacs version. There's an updated one for > 4.5.5 at http://md.chem.rug.nl/~mdcourse/molmod2012/ > Although I'll check again if that bug may still cause problems... If you > stick to .gro format for structures, you're always fine. Only if you want to > use pymol or so, you need to convert it to .pdb. > > Cheers, > > Tsjerk > > On Jul 5, 2012 11:59 PM, "Justin A. Lemkul" <jalem...@vt.edu> wrote: > > On 7/5/12 5:51 PM, jonas87 wrote: > > Protein-water.pdb has the following > line: > CRYST1 75.324 ... > > Sounds about right. > >> I'm using the latest version of gromacs, that means this bug was > >> reintroduced? > > Likely it was not fully fixed; I recall a change to editconf, but maybe > genion needs a look as well. > >> So it is ok to always output to .gro instead of .pdb? > > > Always. > > -Justin -- ======================================== Justin A. Lemkul, Ph.D. > Research Scientist ... > > -- gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-us... -- 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 * Only plain text messages are allowed! * 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
