On Mon, Nov 25, 2013 at 3:40 AM, Andrei Neamtu <neamtuand...@gmail.com>wrote:
> Dear GMX users, > > I am simulating a system of two proteins in TIP4P water box. The > simulations are performed on a system with 3 servers each containing 16 CPU > cores and 2 Tesla 2090 GPU. > The problem thai I encounter is related to the saved interaction energies > in the .edr file and read with g_energy. > > It seems that when using the GPU acceleration none of the interaction > energies are saved for the short-range non-bonded interaction computed on > the GPU. > The SOL (solvent) - SOL LJ-SR and Coul-SR are all ZERO. Also Protein - SOL > are all zero. > When using CPU only accceleration these energies are saved correctly! > Despite the zeroes in the energy file the simulations seems to proceed > correctly when visually inspected. > > I wonder in I do not miss something obvious. > > I am asking if anybody observed a similar behaviour and what should be the > solution to this problem. > > > I upgraded to 4.6.4 version but also on 4.6.1 the problem was still > present. > > Can you clarify if you have re-run the simulation under 4.6.4, not just re-analyzed the energies with 4.6.4 g_energy? Doing the latter will have no effect if the energies were not saved correctly in the original .edr file. http://redmine.gromacs.org/issues/1293 seems relevant here; perhaps multiple energygrps still are not supported on GPU. -Justin -- ========================================== Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 ========================================== -- 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.