[gmx-users] Protein-ligand interaction calculation

[Justin Lemkul]

On 9/11/15 9:46 AM, michael zhenin wrote:
> Hello,
>
> I have simulated (REMD simulation) a protein complexed with a ligand and
> wanted to know if there is any option for calculating the non bonded
> energies between the protein and the ligand (throughout the entire
> simulation).
>

Use energygrps in the .mdp file, regenerate new .tpr, and use mdrun -rerun on 
the existing trajectories.

-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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