[gmx-users] Protein-ligand

[Justin Lemkul]

On 4/19/17 6:50 AM, RAHUL SURESH wrote:
> Dear Gromacs users
>
> how to determine the interaction energy between ligand and protein at each
> frame of simulation?
>

Set appropriate energygrps in the .mdp file, create a new .tpr and use mdrun 
-rerun to recalculate the interaction energies from the existing trajectory. 
This quantity may or may not be physically meaningful, depending on the details 
of the force field.

-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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