[gmx-users] gromacs Bug?

Justin Lemkul jalemkul at vt.edu
Sat Jul 19 12:25:45 CEST 2014



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
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Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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