[gmx-users] g_potential help

[Justin Lemkul]

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

-- 
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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
http://mackerell.umaryland.edu/~jalemkul

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