Now I used mdrun -nt 2 it showed:
Fatal error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off. and mdrun -nt 1 it showed: Program mdrun, VERSION 4.5.4-dev-20110711-dadcb Source code file: /var/local/cache/git-build/gromacs/src/gromacs/mdlib/ns.c, line: 2544 Fatal error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off. On Thu, Dec 1, 2011 at 11:38 AM, lina <lina.lastn...@gmail.com> wrote: > On Thu, Dec 1, 2011 at 7:45 AM, Mark Abraham <mark.abra...@anu.edu.au> wrote: >> On 1/12/2011 3:25 AM, lina wrote: >>> >>> The Y-size of the box (1.999239) times the triclinic skew factor >>> (1.000000) is smaller than the number of DD cells (2) times the >>> smallest allowed cell size (1.000000) >>> >>> I don't understand the fatal error message it has been given during a >>> simple run, >>> >>> I tested with large box already, during editconf I used -d 30 already, >>> >>> it's a very small peptide, the box dimension is 63.95000 60.76600 >>> 62.9990 >> >> Your system may be too small to parallelize over the number of processors >> you are using (and as usual, it would have been a good idea to supply your >> mdrun command line unless you enjoy wasting time when people make wrong >> guesses). > > As you can see it's a very small job, so I just run on laptop, > > now I changed the mdrun -nt 4 > it showed: > Fatal error: > The X-size of the box (3.994507) times the triclinic skew factor > (1.000000) is smaller than the number of DD cells (4) times the > smallest allowed cell size (1.000000) > > > The Fatal error about the Y-size when I used mdrun -nt 8 > > can you guess which is wrong here. on the last email the URL contains > the md.mdp, topol.top and .gro files to run a mdrun. > > Thanks, > >> >> 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