[gmx-users] Help Energy Diferences

[Mark Abraham]

... and stop using 5.0-rc1!

Mark


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
>> different,
>> 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
>
> --
> ==================================================
>
> 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
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
> --
> 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-request at gromacs.org.
>