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

Ricardo O. S. Soares ross_usp at yahoo.com.br
Wed Jun 16 20:09:54 CEST 2010

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...

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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