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

[Justin Lemkul]

On 4/26/15 7:42 PM, Brett wrote:
> Dear Justin,
>
> I mean why the RMSD is such huge. Does it mean in the energy mminimization step the protein has moved from point A to point B which is long long distance away from point A but, although the protein has been continously embedded in water? If the RMSD is above several thousands, it would mean the protein conformation after energy minimization would be absolutely different from the input pdb for the pdb2gmx.
>
> I am looking forward to getting a clarification.
>

Don't confuse the RMSD of the coordinates with the RMSD of the potential energy 
data series.

What gmx energy is printing is what you asked for - an analysis of the potential 
energy, so RMSD here is the RMSD of the energy values.  Even small changes in 
the structure can have very large effects on the energy.  You may go from +10^6 
before EM to -10^6 after EM.  That's 12 orders of magnitude difference in the 
energy, but your protein's RMSD is probably a fraction of an Angstrom.

-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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