[gmx-users] Inconsistency of multicore simulations in Gromacs 4.5.3

Mark Abraham mark.j.abraham at gmail.com
Tue Mar 17 00:38:44 CET 2015


Hi,

What do you mean by "exactly the same?" MD is chaotic, and unless you run
mdrun in its reproducible mode, you will not get reproducibility of a
trajectory. gmxcheck may help you discover what you have actually got.

And you might want to upgrade such a prehistoric version of GROMACS ;-)

Mark

On Mon, Mar 16, 2015 at 10:49 PM, Fei Zhang <feiz at vt.edu> wrote:

> Dear all,
>
> Sorry to interrupt.
>
> I encountered a problem while using Gromacs 4.5.3 with mpi to simulate
> ionic liquid constrained between two constant charged electrodes. However
> when I use 1 core and 32 cores to run same simulation (with same .tpr
> file), the charge density distribution of the first 3000 steps are exactly
> the same, however later, in about 10000 steps, the charge density
> distribution of 32 cores and 1 core become different.
>
> The compiling environment is: 1) gcc/4.7.2    2) openmpi/1.6.4    3)
> fftw/3.3.4(double precision).
>
> I am quite confused about it and wonder if anyone else has encountered the
> same problem.
>
> Best Regards,
>
> Fei
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