Joe Joe wrote:
Hi Justin,
Thanks for helping me with this.
On Sat, Apr 11, 2009 at 4:46 AM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@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
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