[gmx-users] Dielectric constant

[Justin Lemkul]

On 10/20/16 8:51 PM, Thejus Kartha wrote:
> Hello there.
> While calculating the dielectric constant of a mixture of dioxane in water, I am getting really absurd values- a 1% solution has about 101. The command I've been using is the following:
>
> gmx dipoles -f sol1ns2.trr -s sol1ns2.tpr -o dipac.xvg -eps diel_1.xvg -a muavers.xvg -d dipdist.xvg -P 1 -corr mol -c dipcorr.xvg
> Can you tell me where I'm going wrong? And also, if I add the additional option of -epsilonRF 78 with it, the value shoots up to more than 200. How come?

Did you make your molecules whole prior to doing the analysis?

-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 629
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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