Hi Justin, Thanks for helping me with this. On Sat, Apr 11, 2009 at 4:46 AM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > Joe Joe wrote: > >> How do I determine what those values should be? How does it affect the >> simulation? >> >> > The header of your log file should have printed what the initial guesses > were. The -dd option sets how many PP nodes there are in the domain > decomposition; using 4 cores, there are probably 3 PP: 1 PME, so you > probably can't tweak this option, really. I do not get it. the input to -dd is a vector. What to the elements of the vector represent? > > > The -rcon option is explained in mdrun -h or the manual. See what mdrun > guessed, then increase this value. I tried -rcon 3.0 and got the same error. The error only occurs when I do the exchange. If I increase the replex from 500 to 1000 then I do not see the error for 1000 steps. How is the replex associated with the domain decomposition? > > > -Justin > > thanks, >> >> Ilya >> >> >> On Fri, Apr 10, 2009 at 8:00 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> 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 <http://vt.edu> | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> > -- > ======================================== > > 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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