[gmx-users] gromacs Bug?

[Justin Lemkul]

On 7/18/14, 9:56 PM, ANDRES ADOLFO ORTEGA GUERRERO wrote:
> Hi dear Gromacs  users, i would like to report something maybe could be a
> bug or a mistake of me , you´ll see, i run an MD of a System with CNT
> Protein Water and ions, i use a index.ndx file, my CNT doestn´t have any
> charges, but when i check the Coul SR CNT-CNT there were really huge,
>
> so i start a process and run different MD in order to get the problem, and
> , the only way i could Coul SR CNT-CNT 0 as is supposed to be, was when i
> do not use an index file,
> with different simulation where i use the index.ndx file, my energy are
> different ,
>

Then there's your problem - something about your definition of groups is wrong.

-Justin

-- 
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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

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