On 6/21/17 10:55 AM, gozde ergin wrote:
However in the paper they have mentioned that they increased the sigma for amino nitrogen–carboxylate oxygen interactions by 0.13Angstrom relative to the original value. So I assume there should be original value? However you mentioned that there is no pair-specific LJ interaction in OPLSAA. Even if I add a [nonbond_params] what epsilon and sigma should I use? Because they talk about the increment in sigma and I do not know the original value. Maybe I should connect them directly.
Yes, do that to make sure they're consistent with the publication, but combination rules are explained in the PDF manual (and presumably in the original literature for the force field!) so you can calculate these very easily. It's simple arithmetic.
-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.
