Hi Antje,
Just to add some more to Jason's possibly over cautious email. There should
be no problem with you comparing results between AMBER 9 and AMBER 11 (CPU
or GPU) as long as you are running the same simulation parameters. As Jason
said though individual trajectories will diverge. You can even prove this to
yourself by running a simulation with AMBER 9, stopping it and getting the
restart file and then running the 'restarted' simulation twice, once in
serial and once in parallel and you will see things start to diverge.
Neither is 'wrong' though, it is just rounding differences that cause things
to take different paths through phase space. The same will happen with AMBER
11 however you should be perfectly fine to interchange amber 9 , amber 11
CPU and amber 11 GPU within a single run. Just be aware that ultimately you
need to run your simulations long enough that your results converge. This is
irrespective of what version of the code you are using.
All the best
Ross
> -----Original Message-----
> From: Jason Swails [mailto:jason.swails.gmail.com]
> Sent: Friday, April 08, 2011 11:38 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Compare simulations done with AMBER9 to ones done
> with AMBER11 Cuda?
>
> If you run for long enough (i.e. any amount of time worth writing a
> paper
> about ;)), then the results will diverge due to the chaotic nature of
> many-body systems and the limits of machine precision. Thus, the only
> things you can directly compare are ensemble properties averaged over
> an
> entire simulation.
>
> My suggestion would be to re-run some of the simulations you ran with
> Amber9
> with Amber11 CUDA and check that you get the same ensemble results.
> This
> should be a good indication that you can safely move throughout the
> two.
>
> Hope this helps,
> Jason
>
> On Fri, Apr 8, 2011 at 2:45 AM, Antje Wolf
> <antje.wolf.scai.fraunhofer.de>wrote:
>
> > Dear list,
> >
> > I did some simulations with AMBER9. I would like to do an additional
> > simulation with different conditions. As I am running out of time
> with my
> > study, I would like to use AMBER11 CUDA. Now I have some doubts if I
> can
> > compare the results later on. What are your experiences with
> comparing
> > results obtained with different AMBER versions?
> >
> > Your opinion is highly appreciated.
> >
> > Cheers,
> > Antje
> >
> > --
> > Antje Wolf
> >
> > Fraunhofer-Institute for Algorithms and Scientific Computing (SCAI)
> > Department Bioinformatics
> > Schloss Birlinghoven
> > D-53754 Sankt Augustin
> >
> > Tel.: +49 2241 14 2552
> > E-mail: antje.wolf.scai.fraunhofer.de
> > Internet: http://www.scai.fraunhofer.de
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Fri Apr 08 2011 - 12:00:15 PDT
