[gmx-users] genion problem
jalemkul at vt.edu
Mon Oct 5 13:35:46 CEST 2015
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
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 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
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