[gmx-users] SOL LJ and Coul energies

Mark Abraham mark.j.abraham at gmail.com
Wed May 20 09:58:48 CEST 2015


On Wed, May 20, 2015 at 6:08 AM Quentin Kaas <q.kaas at 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).


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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