[gmx-users] Free Energy calculation
Justin Lemkul
jalemkul at vt.edu
Thu Nov 13 19:34:58 CET 2014
On 11/13/14 4:09 AM, RINU KHATTRI wrote:
> hello gromacs users i am working on protein ligand complex with popc
> membrane i want to calculate the free energy of protein and ligand i
> have to follow which tutorial (methane in water) but my protein is
> membrane protein i am also running md simulation (70 ns) i am new in
> free energy calculation from where i have to start after the
> production md or i can start from the original pdb file
The "free energy of protein and ligand" is a rather ill-defined quantity. Are
you trying to calculate binding free energy? If so, there's a huge amount of
literature on this topic. It comes down to simply doing a thermodynamic cycle
of the ligand in water and in the binding site. Restraints might be needed to
keep the ligand bound while being decoupled, but again there's tons of papers on
this topic.
-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
==================================================
More information about the gromacs.org_gmx-users
mailing list