On 7/25/14, 7:39 AM, #SUKRITI GUPTA# wrote:
Dear Gromacs users, I wanted to simulate metal ions in gromacs. For Fe+2, I have lj potential parameters already defined in OPLSAA forcefield, so I wanted to know if I want to add FE+3 in my simulation, then the LJ parameters for it will be different from that of Fe+2 or same? I thought it will be same because vander waals radii is defined for a element and not ion, hence it will be same for Fe or Fe+2 or Fe+3.
In any force field, LJ and electrostatic terms are parametrized to balance in some way that produces some physically sensible behavior. Given the extremely high charge density of Fe2+ and Fe3+, I see no reason to think that the LJ parameters for one would be the same as for the other.
-Justin -- ================================================== 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 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.
