[gmx-users] Gromacs parellal run:: getting difference in two trajectories

David van der Spoel spoel at xray.bmc.uu.se
Thu Sep 11 13:34:25 CEST 2008

vivek sharma wrote:
> Hi There,
> I am running gromacs parellal version on cluster, with different -np 
> options.
> On analyzing the 5 nsec trajectory using ngmx, I am finding difference 
> in the trajectory of two similar runs (only thing varying in two runs in 
> -np i.e 20 and 64 ), where mdp file and input files are same in two cases.
> I am wondering why I am getting this difference in two trajectories ?
> I am looking for the advice whether I did something wrong or what may be 
> the probable reason for this difference.

THis is normal.

In a computer (a+b)+c is not equal to a+(b+c).

> Also, I am not able to run gromacs faster by increasing the -np issue, 
> Is there any max limit for scaling gromacs on parellal cluster ?
This will be fixed in 4.0

> With Thanks,
> Vivek
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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