[Chimera-users] More on initial energy value from Chimera

Thomas Sturgill tws7w at virginia.edu
Thu Dec 20 10:16:47 PST 2012

Elaine has explained that the initial energy is a total energy and not a free energy.  Understood.

I want to verify that a negative energy is "better" than a positive energy, and a more negative energy is "better" still.   This is what I assume now, but I had an 
angst that the energy value is somehow based on absolute value, so the "best" minimized energy is zero.

Humor my question, because I have to be 100% certain.  No need to go into caveats about the ability of Chimera minimization to make models worse, and how 
difficult the energy parameter is to interpret.


Thomas W. Sturgill, M.D.-Ph.D.
Biozentrum, University of Basel
Department of Biochemistry/Hall Lab
Klingelbergstrasse 70
CH4056 Basel, Switzerland
TEL: (+41 61) 267 2172
FAX: (+41 61 267 2149

Visiting Professor
U. of Virginia, Pharmacology
Charlottesville, VA 22908 USA
FAX:  (434) 924-5207

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