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

[Justin A. Lemkul]

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

-Justin

> 
> Thanks a lot.
>  
> ////
> 
> 
> ---
> 
>  
> 
> Ricardo O. S. Soares , MsC.
> Group of Biological Physics - Department of Physics & Chemistry
> Faculty of Pharmaceutical Sciences at Ribeirão Preto - University of São 
> Paulo.
> Av.do Café, S/N - ZIP:14040-903 - Ribeirão Preto, São Paulo,  Brazil.
> Phone: +55 16 36024840.
> 
> 
> ross_usp at yahoo.com.br,rsoares at fcfrp.usp.br
> 
>  
> 
> 
> 
> 
>  
> 

-- 
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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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