[gmx-users] polarizable water and non-polarizable alkanes

Justin Lemkul jalemkul at vt.edu
Wed Jul 9 13:46:23 CEST 2014

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 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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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