[gmx-users] Replica Exchange Error

[Mark Abraham]

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