[gmx-users] Replica Exchange Error

[Joe Joe]

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 <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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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