[gmx-users] g_potential help

[Justin Lemkul]

On 4/21/14, 9:58 AM, rajat desikan wrote:
> Hi All,
>
> I have a membrane-protein-solvent system, and I want the potential across
> the membrane in the direction of the membrane normal. I have 2 questions in
> that regard.
>
> 1) We know that epsilon_r = 80 for the water, ~7 for the membrane-water
> interface and ~2 for the hydrophobic membrane core. g_potential returns the
> result for epsilon_r = 1. How can I incorporate this into the result?
>

I'd venture a guess that the value of epsilon_r in the output is the same as the 
interpretation of epsilon_r in the .mdp file - it is the relative dielectric 
permittivity.  A value of 1 means don't scale anything; see previous discussions.

> 2) Default ng =1? Is the number of groups referring to the number of charge
> groups defined in the topology?
>

No, that means the number of groups you want to analyze, just like g_rdf and 
other tools sometimes give the option of doing multiple analyses at the same time.

-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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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