[gmx-users] Replica Exchange Error

[Joe Joe]

It works just fine without RE.

On Sat, Apr 11, 2009 at 8:49 PM, Mark Abraham <Mark.Abraham at 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 <jalemkul at vt.edu<mailto:
>> 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?
>>
>
> 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 at 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090412/661090b1/attachment.html>