[gmx-users] g_energy reporting 0.0000 interaction energy between energy groups in GPU run?
leandro.obt at gmail.com
Wed Sep 10 03:41:11 CEST 2014
Thank you for your quick answer, Justin.
I'll make new .edr files using only CPUs.
On Tue, Sep 9, 2014 at 10:11 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
>> Consider the following case: I simulated two copies of molecule
>> starting from a structure in which they are non-covalently interacting.
>> using the AMBER99 forcefield with GAFF. I've confirmed by visual
>> 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
>> 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
>> 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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