On 1/12/16 3:19 AM, Turgay Cakmak wrote:
Hi all, I have a quick question about neutralizing the system. I have a solvated system that contains a charged protein of -2q. Is there a major difference betwen adding 2 Na ions and a single Ca ion to neutralize the system (using genion)?
For the purposes of neutralization, probably not, but note that additive force fields do not deal well with divalent ions. Na+ or K+ are preferable if only being used for simple balancing of charge.
-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.
