[gmx-users] binding delta G, H and S for ion-protein

Justin Lemkul jalemkul at vt.edu
Sun Mar 16 20:27:40 CET 2014

On 3/16/14, 2:05 PM, Andrew Bostick wrote:
> Dear Justin
> Thanks for your answer.
> All of methods you mentioned ( PMF, TI, FEP, BAR) are used for calculating
> free energy (G). In addition to free energy (G), I want to calculate
> enthalpy (H) and entropy (S).
> Are you sure can I use above methods for calculating both of enthalpy (H)
> and entropy (S)?

There are two separate questions at hand here.  The first is: which method for 
calculating free energies is appropriate to the system at hand?  The second is: 
how do I do that in Gromacs?  I can't help you with the first; no one on this 
list can because there's too much that we don't know.  Your job is to survey the 
literature and consult with colleagues/supervisors for recommendations. 
Studying ion binding to proteins is not a new idea.  Once you have a direct 
approach that you wish to use within Gromacs, that's where those of us on the 
list can help.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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