[gmx-users] Free energy calculations with membrane

[Justin Lemkul]

On 11/17/16 12:48 PM, Live King wrote:
> Hi everyone,
>
> I am trying to do Justin's thermodynamic integration tutorial with a lipid
> bilayer. I believe the energy I will get from this exercise is the energy
> required to take alanine from membrane to vacuum. I have placed my alanine
> at the center of bilayer. Does this energy output contain contribution from
> both alanine-lipid and alanine-water interactions? or just alanine-lipid
> interactions.
>

You're decoupling alanine from everything.

-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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