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

[Justin Lemkul]

On 12/15/16 10:15 AM, Alex wrote:
> 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.
>

Are there significant interactions between the amino acid and Na+, and/or the 
surface and Na+? If so, the only way to figure out the extent of the 
contribution is a full thermodynamic cycle in which the amino acid and Na+ are 
decoupled separately.

-Justin

> Regards,
> Alex
>
> 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
>>
>> ==================================================
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>

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

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

==================================================