# [gmx-users] Questions about free energy calculation tutorial

Justin Lemkul jalemkul at vt.edu
Sun Nov 6 13:27:20 CET 2016

```
On 11/5/16 11:51 AM, Alex wrote:
> Hi,
> Concerning to the Na+ charge, if we were interested in the relative binding
> free energy in a system (\Delta\Delta G), I mean the difference between two
> Free energy in the Ligand and Complex situations, then could you please
> confirm me that you can make uncharged the the Na+ along with your ligand
> in a single couple-moltype under perturbation, if and only if you do it in
> both ligand and complex free energy calculations, because the effect of Na+
> however is being treated could cancel out each other in the thermodynamic
> cycle of \Delta\Delta G.
>

Yes, that should cancel out.

-Justin

> Regards,
> Alex
>
> On Sat, Nov 5, 2016 at 3:43 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 11/4/16 8:44 AM, gozde ergin wrote:
>>
>>> Thank Justin, ok I understand now.
>>> Then I need to run the simulation with +1 charge, since I made 0 of all
>>> the charges in SDS, Na+ charge will stay there.
>>> Do you think it is ok run with +1 charge?
>>>
>>>
>> Systems with net charge can be accounted for by the neutralizing plasma in
>> PME. Whether or not that affects your results depends on the nature of the
>> system, but for a small molecule in a homogeneous medium like water, any
>> artifacts should be well below the error inherent in the free energy
>> calculation itself. Just make sure whatever transformation you perform is
>> analogous to what's measured experimentally.  If you need the total free
>> energy of hydration for NaSDS, you can just decouple SDS in water with no
>> Na+ and sum the two contributions (SDS and Na+ separately).  If you just
>> want the SDS hydration free energy, decouple it in a box of pure water.
>>
>> -Justin
>>
>> On 04 Nov 2016, at 13:36, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>
>>>> No, you should not.  The topology you posted before had Na+ as part of
>>>> the SDS [moleculetype] and you were decoupling the whole thing.  This is
>>>> what I am saying you should not be doing if you're trying to get just the
>>>> hydration free energy of SDS.
>>>>
>>>> -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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--
==================================================

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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