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

Alex alexanderwien2k at gmail.com
Thu Dec 15 16:16:28 CET 2016

Thanks Justin for your response.

Surly PMF is better, but the point is that via FEP I have already calculate
the binding free energy of a charged amino acid to a solid surface while
Na+ used as counter-ion where both "amino acid and Na+" considered as a
single "couple-moltype" to be decoupled both of them simultaneously from
the system. And of course by this I have desolvation energy of Na+ into
account which should not be. So, I want to calculate the desolvation energy
of only Na+ to remove its portion out from my original calculation. That is
why I want to keep the conditions as my original simulations.

 With free energy of {amino acid and Na+} in both bounded and unbounded to
the solid slab, I mean DG_unbounded{AA and Na+} - DG_bounded{AA and Na+},
the portion of Na+ has been already removed partially, but not completely.


On Thu, Dec 15, 2016 at 3:55 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> 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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