[gmx-users] Binding energy calculation

[Justin Lemkul]

On 9/13/15 8:56 AM, Malihe Hasanzadeh wrote:
> Hi
>
> I have simulated a protein-ligand with gromacs and submitted it. My
> reviewer asked me about calculation of binding energy. Which tutorial is
> acceptable and suitable for me to do it?

Either free energy calculations (alchemical transformation) or PMF.  Note that 
you will need to use the new [intermolecular_interactions] in version 5.1 to use 
the free energy code and get a meaningful free energy of binding.

-Justin

-- 
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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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