[gmx-users] Gromacs in Parallel

[David]

On Wed, 2005-08-17 at 15:34 -0400, Shrivastava, Indira wrote:
> Hi,
> 
>  
> 
> I am doing some GROMACS simulation test runs on AMD Opteron 246 nodes
> cluster. I ran the job on one node and two nodes.
> The trajectories of the one node and two nodes jobs are slightly
> different, even though the initial system was identical in all
> respects for both the jobs (one node and two nodes) as seen from the
> rmsd’s and rmsf’s for the protein, over a period of less than 1ns (600
> ps). 
> 
> Can anyone tell me whether this is a hardware or software problem?
This is inherent numerical problem since e.g. numerically
a+(b+c) is not equal to (a+b)+c

The trajectories should in principle give the same averages.

> 
>  
> 
> Thanks
> 
> Indira   
> 
>  
> 
>  
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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