[gmx-users] Gromacs on GPU

Ben Hall benjamin.a.hall at ucl.ac.uk
Fri Jan 27 18:18:08 CET 2012


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


Dr Benjamin A Hall
Centre for Computational Science, Department of Chemistry, UCL
benjamin.a.hall at ucl.ac.uk

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