[gmx-users] divergent energy minimization results from identical starting system

Matthew Chan mchan3 at connect.carleton.ca
Sat Jan 29 00:17:16 CET 2011


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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