[gmx-users] different results in different machines

[David van der Spoel]

On 2/11/10 7:40 PM, Rebeca García Fandiño wrote:
> Hi,
> I am doing PMF calculations using Gromacs 3.3.3, and I have found very 
> different results using 2 different machines.  Attached you can see 
> that the graphics are really different for both cases (about 10 
> KJ/mol!!). The version of Gromacs (3.3.3) and number of processors 
> used (2) is the same for both calculations. The .tpr files and all the 
> starting files are identical for both calculations. The only thing 
> that changes is the machine where they were carried out.
> I have checked the energy files for both cases, and they are 
> different, but taking into account the stochastic effect, I suppose it 
> is normal. There are slight differences in the energies in the step 0 
> for some of the windows (but in the 5th decimal number, so they should 
> not be important, I suppose). Any idea of the cause of the problem? 
> Has anyone experienced similar problems? Any suggestion will be much 
> appreciated.
> Thanks a lot for your help, in advance.
> Cheers,
Without error bars it is very hard to judge how different these are. Can 
you add errorbars?
How long are the simulations at the individual data points?
>
> Rebeca Garcia
>
>
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
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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