[gmx-users] genion problem

[Justin Lemkul]

On 10/5/15 2:26 AM, Golnaz Roudsari wrote:
> Dear all
> I want to use bromide for neutralize my system. I wrote genion -s ions.tpr
> -c file.gro -p topol.top -pname K -nname BR -nn 24. After I cheked it the
> gromacs read Boron intead of bromide. I wrote command -nname BR -nn 24. and
> I did not use K but in all cases my output was boron and I did not see any
> Bromide.

Something doesn't add up.  But the only force field that supports Br- is 
OPLS-AA, so if you're using any other force field, whatever genion writes may 
not be correct or even supported by the force field.

-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 629
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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