[gmx-users] Questions about free energy calculation tutorial

[Alex]

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.

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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