[gmx-users] Replica Exchange Error
ilchorny at gmail.com
Mon Apr 13 04:12:24 CEST 2009
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
> 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 .
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