[gmx-users] Questions about free energy calculation tutorial

Justin Lemkul jalemkul at vt.edu
Sun Nov 6 13:44:16 CET 2016

On 11/6/16 7:38 AM, gozde ergin wrote:
>> 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
> Thanks Justin,
> I have difficulty to understand NaSDS? SDS is Sodium dodecyl sulfate so Na is in this molecule.
> What about running the simulation with both Na ions and dodecyl sulfate inside the water. However I just decouple the dodecyl sulfate part.
> I also make the charge of Na ions zero so I can run the simulation with net 0 (zero) charge.
> Na ions will physically be there but their charge will be zero.

What physical significance does an uncharged Na have?

> Is not this more closer to experimental SDS hydration state?

Under what conditions was the hydration free energy determined?  You have to 
model something relevant.  SDS is only anionic because it is acidic.  Is the 
experimental value obtained from the acid itself, or the salt?  If the former, 
then you need to deal with H+ solvation and changing protonation state in gas 
vs. aqueous phase.  If it's the salt, then take the known Na+ value for the 
force field and add it to the SDS value you obtain at infinite dilution. 



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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