[gmx-users] MVAPICH2 mdrun problem for SD and MD, GROMACS 4.0.5

Mark Abraham Mark.Abraham at anu.edu.au
Sat Oct 31 00:19:39 CET 2009

Daniel Adriano Silva M wrote:
> Mark,
> Then I will try with other versions, check gmx-tests and not mix
> compilers, thank you much by your help. Last question, I am afraid to
> ask, but I have some simulations that were ran with this setup,
> energy, temp, and pressure looks good on all, and it ran by pretty
> long time (several ns) without any apparent errors, do you think that
> there could be any way to check if these md-sims results are actually
> wrong?

That's a hard question, because MD with even the same GROMACS version 
with different compilers can diverge rapidly. If you still had the old 
version, you might try a new mdrun -reprod with nstlog=1 on both 
versions. If they give the same output, you might then have some 
confidence that the old version was only wrong under some conditions, 
and hopefully all of those provoked crashes. However it would be likely 
that they wouldn't give the same output even if both were functioning 
correctly. Still, the energy differences over the first few MD steps 
should be down at about the precision reported in the .log file, and 
that's useful knowledge.


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