[gmx-users] Replica Exchange Error

[Justin A. Lemkul]

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.

The -rcon option is explained in mdrun -h or the manual.  See what mdrun 
guessed, then increase this value.

-Justin

> thanks,
> 
> Ilya
> 
> On Fri, Apr 10, 2009 at 8:00 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at 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
> 
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-- 
========================================

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

========================================