[gmx-users] Fw: mpirun

[Justin A. Lemkul]

fahimeh baftizadeh wrote:
> 
>     sorry I forgot to add that the random seed for the velocity is the
>     same in all the tprs and the random seed for the thermostat is also
>     the same.
>     and if I redo the simulation with only one processor, the results
>     are always identical. but not with more than one.
> 
>     Do you think is it due to the comunication of the processors together?!
>     Thanks

You will find some useful material here:

http://www.gromacs.org/Documentation/Terminology/Reproducibility

There are also several relevant discussions in the list archive.  You can try to 
force some measure of reproducibility with mdrun -reprod.  MD is chaotic, so any 
small change can cause a big difference down the road, so to speak.

-Justin

> 
>     Fahimeh
> 
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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