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) > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.