[gmx-users] Gromacs on GPU

Matthew Lardy mlardy at gmail.com
Fri Jan 27 18:52:55 CET 2012

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.


On Fri, Jan 27, 2012 at 9:18 AM, Ben Hall <benjamin.a.hall at ucl.ac.uk> wrote:
> Hi
> I've been attempting to use the GPU enabled version of gromacs to run
> implicit solvent simulations, but I've run into an odd problem. I have
> downloaded and can run the benchmark simulations from the gromacs website,
> and reproduce the speeds reported there. However, when I edit the MDP
> files to write out data both the xtc and trr files contain junk data- the
> first frame is correct but every coordinate in the following frames is the
> same. These same MDP files work on the GPU disabled (default) gromacs and
> produce reasonable trajectories. As the simulations aren't crashing I
> assume that the issue relates to writing specifically; has anyone observed
> the same problem, and is there a workaround or patch?
> The versions of each piece of software used are
> gromacs 4.5.5
> openmm 3.1.1
> cuda 4.0
> and all compiled using intel compiler version 11.1/072
> Thanks in advance
> Ben
> --
> Dr Benjamin A Hall
> Centre for Computational Science, Department of Chemistry, UCL
> benjamin.a.hall at ucl.ac.uk
> --
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