[gmx-users] 5 identical simulations --> 5 different results, why?
mrshirts at gmail.com
Wed Jun 16 20:32:33 CEST 2010
Things to check: were the random numbers initializing the velocities
the same? Looking at the log files for each simulation should be able
to tell you (look at the initialized kinetic energy at the beginning).
Some options choose a different random number automatically for each
On Wed, Jun 16, 2010 at 12:09 PM, Ricardo O. S. Soares
<ross_usp at yahoo.com.br> 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...
> 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
> 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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