[gmx-users] Replica Exchange Error

Justin A. Lemkul jalemkul at vt.edu
Sat Apr 11 05:00:05 CEST 2009

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?


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 A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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