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


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