[gmx-users] ligand binding

[Justin Lemkul]

On 8/7/14, 8:47 AM, Meenakshi Rajput wrote:
> Thank you Justin. Please tell me if emtol should be 1000 or 100 for albumin

There are no hard and fast rules when running normal MD simulations.

> protein complex? As for emtol=1000, complex(mentioned in the tutorial) is
> converged in some steps and graph plotted for potential energy shows sudden
> downfall. Please tell me what is the reason behind this?
>

If there is a dramatic decrease in energy, there should be an obvious structural 
change somewhere.  Watch the trajectory.

-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 601
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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