[gmx-users] interaction between ligand and protein

[Justin Lemkul]

On 11/30/14 11:57 AM, Mahboobeh Eslami wrote:
>   hi GMX users
>
> i have simulated the protein-ligand complex by gromacs for 20ns. Which configuration should be chosen for the study of interactions between proteins and ligands?
>

Why choose one configuration when you have a whole trajectory's worth of data? 
That's the principal advantage of the simulation - you study dynamic behavior. 
A single snapshot rarely, if ever, tells the whole story.

-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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