[gmx-users] It appears that the Claim that NAMD works with gromacs is false

David spoel at xray.bmc.uu.se
Sun Jul 17 10:28:51 CEST 2005

On Sat, 2005-07-16 at 19:09 -0400, Jim Kress wrote:
> I've tried several of the simple examples provided by the gromacs people,
> using the directions found in the NAMD user guide.  To date I have been
> unable to get them to work.  I admit it may be user error but I have yet to
> find one.
> I'd be more than happy to provide more info to anyone off the list who
> claims to have been able to use gromacs top and gro file to run NAMD
> simulations since the scaling of gromacs is poor compared to NAMD but the FF
> set is more encompassing.

NAMD scaling is great, largely because the single processor code is so
slow. Try running your system on a single processor with gromacs and on
four or eight with NAMD and compare the performance.

I can't help you with your question though, sorry about that. I wasn't
even aware of the possibility.

> Any help would be appreciated.
> Jim Kress
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
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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