Hi,
On Wed, May 20, 2015 at 6:08 AM Quentin Kaas q.k...@imb.uq.edu.au wrote:
Dear all,
I am trying to compute the interaction energy between a small peptide
and water from a short MD simulation (54a7, reaction-field, Verlet, GPU,
gmx 5.04, 1 peptide, 3200 SOL molecules). I have specified SOL and
Protein as energy groups. Contrary to my expectations, LJ and Coul
energies outputed by 'gmx energy' for SOL-SOL and Protein-SOL are all
zero. Is that normal or is it a known bug ?
That's normal. Energy groups are not supported on GPUs (there's a note
printed to the .log file) because we haven't thought of a good way to
implement that on GPUs. A better workflow for this is to use mdrun -rerun,
and in 5.0.5 we fixed rerun + energy groups to choose to use only the CPU,
since the GPU isn't useful (or implemented).
Mark
Best wishes
Quentin
http://cybase.org.au/
PS: The LJ and Coul energies of Protein-Protein are not zero. Simulation
ran fine and was stable (rms and total energy)
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