[gmx-users] Help Energy Diferences
mark.j.abraham at gmail.com
Wed Jul 23 21:53:05 CEST 2014
... and stop using 5.0-rc1!
On Tue, Jul 22, 2014 at 1:17 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 7/21/14, 1:30 PM, ANDRES ADOLFO ORTEGA GUERRERO wrote:
>> Hi Dear Gromacs Users,
>> I have been dealing with a problem, i run an MD of my sistem , and i see
>> problems with my energies due to one of my molecules is a CNT and has no
>> charges and its Coul SR are huge, well i though this could be of an error
>> in my NDX file ,
>> the thing is that i run my MD in my laptop (Mac OS) for really short time
>> and there were no mistake, and when i do the MD in my Work (2 Linux
>> Computer with GPU Nvidia) with the same files, my energy are totally
>> the version is Gromacs 5-0 rc1,
>> Could you help me with this?
> IIRC multiple energygrps are not supported on GPU, so whatever the .edr
> file thinks is CNT-CNT or whatever else is just the energy of the whole
> system. This is a known issue. If you do a run on GPU, don't use multiple
> energygrps, just post-process the trajectory with mdrun -rerun and a .tpr
> file that has the desired groups.
> 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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