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
