[gmx-users] g_energy reporting 0.0000 interaction energy between energy groups in GPU run?

Justin Lemkul jalemkul at vt.edu
Wed Sep 10 03:11:36 CEST 2014

On 9/9/14 9:09 PM, Leandro Bortot wrote:
> Dear users,
>       I did some simulations of organic molecules in solution to study how
> they interact, but I'm facing some problems and your help would be greatly
> appreciated.
>       Consider the following case: I simulated two copies of molecule "AcO"
> starting from a structure in which they are non-covalently interacting. I'm
> using the AMBER99 forcefield with GAFF. I've confirmed by visual inspection
> that the molecules are interacting with each other, i.e. they didn't
> separate during the simulation. Additionally, I've specified the energy
> groups "aco_1", "aco_2", "SOL", "Ion" in the original MD tpr. The problem
> is that g_energy reports all "aco_1-aco_2" energy terms as exactly
> 0.000000. The energy terms are OK.
>       This was only an example. I actually simulated 2, 3 and 4 copies of
> interacting molecules in different ways and this happens in all cases.
>       These results were obtained using GPUs. I used the same .tpr to rerun
> the .xtc on CPUs only and now the "aco_1-aco_2" energy terms are OK. In
> both cases I used GROMACS 4.6.6.
>       I've searched the list but found nothing. Is this a problem/bug? Am I
> doing something wrong with the GPUs?

Multiple energygrps are not supported on GPU.  This should be disabled in 5.0.1, 
and if not, hopefully the next release, as it is a known issue.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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