[gmx-users] Replica Exchange Error

[Joe Joe]

Hi Justin,
Thanks for helping me with this.

On Sat, Apr 11, 2009 at 4:46 AM, Justin A. Lemkul <jalemkul at 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 <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
>
> ========================================
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