[gmx-users] free energy calculation

[Justin Lemkul]

On 10/20/14 6:16 AM, RINU KHATTRI wrote:
> hello gromacs users i am working on protein complex with popc membrane
> i want to calculate the free energy of complex i have run protein
> complex and  dppc tutorial   how to start for that i am using 4.5
> version of gromacs should i use
>
> GROMACS Tutorial Free Energy Calculations: Methane in Water
>
> kindly help
>

Your question is ill-defined.  Free energy of what?  If you're looking for free 
energy of ligand binding, the fact that the protein is in the membrane is of 
little practical difference to any other protein-ligand complex.  Compute a full 
thermodynamic cycle in the binding site, and one in water, and take the difference.

The methane-in-water example is the basic idea, and discusses the process for 
full cycles on ligand systems, but doesn't illustrate it explicitly.  There's 
tons of literature on this topic, though.

-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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