[gmx-users] divergent energy minimization results from identical starting system
roland at utk.edu
Sat Jan 29 00:29:02 CET 2011
are you running in parallel (either MPI or threads)? Load-balancing is one
reason for different rounding errors.
You can run with "mdrun -reprod" to avoid any different rounding between
runs and should in general get the same then.
On Fri, Jan 28, 2011 at 6:17 PM, Matthew Chan <mchan3 at connect.carleton.ca>wrote:
> My second question is about the divergent energy minimization results which
> I have been receiving.
> I've taken the 1AKI lysozyme and prepared a single em.tpr file (1AKI is in
> vacuum). Afterwards I make 10 copies of the em.tpr file and use mdrun on
> each one. If I set the stopping condition to less than 1000kJ/mol nm, my
> potential energies and final structures from each run are not identical.
> I've tried both steepest descent and cg methods for minimization. I've also
> checked that the Fmax is indeed less than my stopping condition, and the
> potential energy is negative. Is this problem well documented or is there
> something wrong with my system? There seem to be a few parts of the manual
> that allude to the possibility of variance between subsequent runs of EM.
> If this is a well documented problem, can someone try explaining the cause
> to me please? I would like to learn more about this topic.
> Also, the potential energy value reported seems to be several orders of
> magnitude different from what other programs are reporting (24 000 vs 500).
> What units are it expressed in?
> Thanks in advance for your replies,
> Matthew Chan
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