[gmx-users] free energy calculation
jalemkul at vt.edu
Mon Oct 20 14:40:29 CEST 2014
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 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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