[gmx-developers] Gromacs on Mare Nostrum (Barcelona Supercomputing Centre)
tsjerkw at gmail.com
Mon Apr 16 13:12:23 CEST 2007
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...
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...
> 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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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
3584 CH Utrecht
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