How do I determine what those values should be? How does it affect the simulation? thanks,
Ilya On Fri, Apr 10, 2009 at 8:00 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Joe Joe wrote: > >> Hi All, >> >> I get the following error when running replica exchange. I have 32 >> replica's with each replica running on 4 processors (128 total). How do I >> decrease the domain decomposition cell size, -dss? What should I set it to? >> > > <snip> > > You're getting some hints from mdrun, I'd start there: > > ------------------------------------------------------- >> Program mdrun_mpi, VERSION 4.0.4 >> Source code file: domdec_con.c, line: 679 >> >> Fatal error: >> DD cell 5 0 0 could only obtain 96 of the 108 atoms that are connected via >> vsites from the neighboring cells. This probably means your vsite lengths >> are too long compared to the domain decomposition cell size. Decrease the >> number of domain decomposition grid cells or use the -rcon option of mdrun. >> ------------------------------------------------------- >> > > ...So manually set -dd and/or -rcon. > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >
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