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

Matt Chan talcite at gmail.com
Sat Jan 29 07:15:01 CET 2011

Hi Roland,

Ah, the -reprod option makes everything consistent between runs now. The 
term 'binary reproducibility' in the help message was a bit confusing at 
first, but I found the wiki page on reproducibility.

Thanks for your help,

On 01/28/2011 06:29 PM, Roland Schulz wrote:
> Hi,
> 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.
> Roland
> On Fri, Jan 28, 2011 at 6:17 PM, Matthew Chan 
> <mchan3 at connect.carleton.ca <mailto:mchan3 at connect.carleton.ca>> wrote:
>     Hi,
>     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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