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 -- ================================================== 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 jalem...@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-requ...@gromacs.org.
