[gmx-users] Replica exchange shell script
Mark.Abraham at anu.edu.au
Mon Feb 27 07:34:16 CET 2006
Sukit Leekumjorn wrote:
> Thank you very much Mark
> I got REMD to run now but I ended up having the same problem as the
> other users had in the past. Below is the error message. I got this to
> run for 2 nodes. For 4, 6, and 8 nodes, the below error shows up in the
> log files. I did try several suggestions from the mailing list, but I
> could not get it to runs more than 2 nodes. Any suggestion in fixing
> this problem would be greatly appreciated. Here is the executable
> command line I used:
Is there anything about your hardware that might be having an effect
after 2 nodes/processors?
> export EXEC="$FF/mdrun_3.3_gcc_mpi -multi -np 8 -replex 200 -s dpp.tpr
> -deffnm dpp"
> I did try removing -multi but did not work. I also "grompp" the .mdp in
> the double precision mode (floating problem), but still did not work.
What was your .mdp file and how did you call grompp?
> Repl 0 1 2 3 4 5 6 7 Repl T 340.0
> 345.0 350.0 355.0 360.0 365.0 370.0 375.0
As an aside, a linear increase of temperatures will see relatively many
swaps between higher pairs of temperatures than lower pairs, because the
distribution of pairs of ensembles that differ by Delta T overlap more
with increasing T. You might want this for some reason I can't think of
at the moment, but an exponential increase of temperatures will see a
(more) linear distribution of exchange frequencies over the T range. You
also get to access higher temperatures for a given ratio of the lowest
two temperatures. Generating an exponential sequences is easy of course,
with T3 = T2 * (T2/T1)
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