[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 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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