On 7/9/14, 3:56 AM, Yana Tsoneva wrote:
Dear colleagues, I am running simulations using Gromacs - 4.6.5 and my systems consist of water/different oils. Until now I have used TIP4P water model and amber99 for the alkanes. I need to run the same simulations, but with a polarizable water model. I succeeded in simulating pure polarizable water (sw-rigid of van Gusteren), but now I have problems adding the alkanes. I know that I should not mix different force fields, but is there any chance for me to simulate polarizable water and non-polarizable alkanes? If there is one, can you tell me how to do it? I read that there is a modification of the CHARMM force field to simulate alkanes with Drude oscillators. Is this the way to achieve compatibility of the force fields?
The CHARMM Drude FF for alkanes was parametrized against SWM4-DP, not SW, so such a combination is not valid. You need a self-consistent force field. I doubt that an additive model of alkanes in conjunction with a polarizable model of water would be reliable.
-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.
