[gmx-users] Gromacs on GPU

[Justin A. Lemkul]

Matthew Lardy wrote:
> Sorry to hear that, as I have had the same problem for over four
> months (OpenMM 3+, Gromacs 4.5.4+, Cuda 4, etc.).  No one ever got
> back to me, and I just abandoned Gromacs for Amber (who's GPU
> accelerated code base compiles and works).
> 
> I would be interested to hear if the intervening time, if a plan had
> been hatched to make the GPU code production quality.  If that has
> indeed happened.
> 

I don't see a corresponding issue posted to redmine.gromacs.org - has there been 
one filed?  If not, reports often get lost on the mailing list, so the only way 
to ensure action is to post a bug report.

We get junk output with 4.5.4 if the box size is set to zero, for some odd 
reason, though in principle it should be ignored with "pbc = no" in the .mdp 
file.  Using any non-zero box results in usable results.  Our OpenMM version is 
the same, but Cuda is in the 3.x series (can't remember off the top of my head, 
sorry).

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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