[gmx-developers] Gromacs on Mare Nostrum (Barcelona Supercomputing Centre)

[Xavier Periole]

Hi Tsjerk,

I also saw this report, which seemed to me a bit strange as they
recently reported extensive simulations using GROMAS (Rueda M,
Ferrer-Costa C, Meyer T, Perez A, Camps J, Hospital A, Gelpi JL,
Orozco M. A consensus view of protein dynamics. PNAS. 2007;104(3):796-801.)
Note however that they used a serial version of GROMACS in the paper.

I do not think that this report means much. They explain very
little about their setup and protocole, which might explain the
deviation from the exp structure.

I am in contact with somebody using the Mare Nostrum, that would be
useful to get a working version on it! Did you install one?

Best,
XAvier

> Actually, these were my sentiments too. It's a bit cheap to suggest
> that gmx just does weird, without further investigation and without
> trying to contact you guys. Of course, I won't suggest that there are
> _no_ bugs in gmx :p But unfolding like that...
> 
> Tsjerk
> 
> On 4/16/07, Erik Lindahl <lindahl at cbr.su.se> wrote:
>> Hi Tsjerk,
>>
>> We'll get in touch with them, but considering we've run tons of
>> protein in parallel without unfolding even with v 3.2.1, I think it's
>> more probably that this is an error with the compiler/setup/user.
>>
>> We can't rule out a bug of course (in particular since PPC970 + IBM
>> compilers isn't such a common combination), but we're a bit irritated
>> that they don't even seem to have bothered getting in touch with is
>> to get help before claiming it's a bug...
>>
>> Cheers,
>>
>> Erik
>>
>> On Apr 16, 2007, at 9:43 AM, Tsjerk Wassenaar wrote:
>>
>> > Dear developers,
>> >
>> > Here is a link to a technical report comparing three different MD
>> > suites, including Gromacs (3.2.1/ffG43a1/PME), on the Barcelona
>> > supercomputer. I'd appreciate if one of you could give it a glance and
>> > a reaction. They mention consistent unfolding of proteins when using
>> > multiple processors.
>> >
>> > http://www.bsc.es/media/809.pdf
>> >
>> > In the report they mention additional data on-site, but I haven't
>> > found it yet.
>> >
>> > I'll put in a request to check 3.3, but would like some additional
>> > input. There may also be added value in contact between the Gromacs
>> > crew and the Mare Nostrum one, but that may be considered later. Note
>> > that these efforts are done within the framework of DEISA and that the
>> > outcomes may be of some significance for the use of Gromacs.
>> >
>> > Cheers,
>> >
>> > Tsjerk
>> >
>> > --
>> > Tsjerk A. Wassenaar, Ph.D.
>> > Junior UD (post-doc)
>> > Biomolecular NMR, Bijvoet Center
>> > Utrecht University
>> > Padualaan 8
>> > 3584 CH Utrecht
>> > The Netherlands
>> > P: +31-30-2539931
>> > F: +31-30-2537623
>> > _______________________________________________
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>> > gmx-developers at gromacs.org
>> > http://www.gromacs.org/mailman/listinfo/gmx-developers
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>>
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>>
> 
> 
> -- 
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
>F: +31-30-2537623
> _______________________________________________
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the www interface 
>or send it to gmx-developers-request at gromacs.org.

-----------------------------------------------------
XAvier Periole - PhD

1- Institute of Molecular Assemblies
      City University of New York - USA
2- Molecular Dynamics-Group
      University of Groningen - The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------