[gmx-users] 5 identical simulations --> 5 different results, why?

[Mark Abraham]

----- Original Message -----
From: Dmitri Dubov <ddubov at ngs.ru>
Date: Thursday, June 17, 2010 13:43
Subject: Re[2]: [gmx-users] 5 identical simulations --> 5 different results, why?
To: "Justin A. Lemkul" <jalemkul at vt.edu>, Discussion list for GROMACS users <gmx-users at gromacs.org>

 
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> Hi, Justin.
 


 
> You wrote:
 


 
> > Ricardo O. S. Soares wrote:
 
>> Hello dear users,
 


 
> >> in order to introduce Gromacs to a few students, I'm taking five 
 
>> computers with the same operational system (ubuntu), to run the same 
 
>> simulation independently. I prepared a box o water and ran all standard 
 
>> steps until the grompp. This is when I copied and pasted the folder to 
 
>> the other four computers. So I ran the same grompp command in each unit, 
 
>> and then the mdrun step. At the end we obtained 5 slightly different 
 
>> results for total energy, pressure, volume etc. Since MD is a 
 
>> deterministic process, one may expect to find the same results for the 
 
>> same simulations. So does anyone have a clue at which step is it 
 
>> possible that those little differences are being brought into the 
 
>> systems? I'm guessing the grompp step...
 


 
> > This page may have some useful information for you:
 


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


 
> It says that
 


 
> "As of GROMACS 4, mdrun -reprod will eliminate all sources of
 
non-reproducibility that it can, i.e. same executable + same shared
 
libraries + same run input file + same command line parameters will lead to reproducible results."
 


 
> In addition:
 
The last condition should be applied not only to gmx parameters themselves. For instance, paralleling the same run between different numbers of my Intel Quad cores gives me slightly different energies too. For small systems about hundreds of atoms this is the case even with -reprod and under relatively long, 10 ns, simulations. 





This is normal, and its behaviour covered in the second dot point on that page.




Mark

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