It works just fine without RE. On Sat, Apr 11, 2009 at 8:49 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote:
> Joe Joe wrote: > >> Hi Justin, >> >> Thanks for helping me with this. >> On Sat, Apr 11, 2009 at 4:46 AM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> 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? >> > > If the problem only occurs at replica exchange steps, then something is > wrong with the interaction of at least two of RE / virtual sites/ DD. Try > the same (multi-)simulation twice, once without replica exchange and once > using particle decomposition to troubleshoot . > > Mark > > _______________________________________________ > 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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