[gmx-users] Desolvation or hydration free energy of an ION

[Justin Lemkul]

On 12/15/16 9:39 AM, Alex wrote:
> Hello gromacs user,
>
> I was wondering if anybody has experience with the hydration or desolvation
> free energy of an ION for example Na+, using alchemical free energy
> perturbation method?
>
> Actually in my case, I would like to calculate the difference between free
> energy of "Na+" when it is close to a solid slab in aqueous solutions,  and
> when it is far away from the slab inside bulk water.
>

If it's a simple matter of Na+ partially desolvating to bind to the surface 
(with no intervening waters) then the simple approach is a PMF.  Using a 
decoupling method requires additional restraints that have to be accounted for. 
This can of course be done done but a PMF is trivial to set up.

-Justin

-- 
==================================================

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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