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

[vivek sharma]

Thanks david for your reply.

Can you tell me up to how many -np value current version of GROMACS can be
optimized (or will reduce the simulation time) ?

Also, how can I test the accuracy of my process when I can't get same result
with similar option (while scaling )?

With Thanks,
Vivek

2008/9/11 David van der Spoel <spoel at xray.bmc.uu.se>

> 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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