[gmx-users] a question related to gmx energy minimization

[Justin Lemkul]

On 4/26/15 9:53 AM, Brett wrote:
> Dear Tsjerk,
>
> Will you please explain to me why the RMSD in this step is so large? For this reason I think there is something wrong.
>

No, there's nothing wrong; the analysis in this case is meaningless.

Energy minimization inherently makes large (orders of magnitude in many cases) 
changes to the potential as the structure is relaxed.  An average energy over 
the course of this process has absolutely no physical meaning.

-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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