On 4/21/14, 5:11 PM, rajat desikan wrote:
Hi Justin, So different parts of my system in Z-direction should be scaled differently, right? On a coarse level, aqueous part with a scaling of 80, membrane with a scaling of 2? How do I correct for this? Can I take the quantitative output for potential difference across a membrane in water from g_potential literally?
You don't need to scale anything. The force field parameters for every biomolecular force field that I know of are based on epsilon_r = 1, i.e. no special alteration of vacuum permittivity. The results, at face value, should be sufficient.
-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.
