[gmx-users] Questions about free energy calculation tutorial

Justin Lemkul jalemkul at vt.edu
Sat Nov 5 15:43:48 CET 2016

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.


>> 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


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