[MMTK] Re: Modes mouvement characterization

khinsen at cea.fr khinsen at cea.fr
Tue Sep 13 18:55:26 CEST 2005


On Sep 13, 2005, at 18:07, Matias Saavedra wrote:

> How can i determine the nature of the mouvements
> described by each of the lowest normal modes
> (direction, collective-concerted, iris-like, bending,
> twists, translations, rotations, rigid body regions
> and their concerted mouvements, etc.) ?
>
> I have to combine the data from displacements and
> deformation energy in some way?

The deformation energy is a global measure of the collectiveness of the 
mode, but it does not describe the nature of the motions. For that, you 
have to look at the displacements.

Techniques for analyzing the displacements in terms of particular 
motion types are described in

	K. Hinsen, G.R. Kneller
	Projection methods for the analysis of complex motions in 
macromolecules
	Mol. Sim. 23, 275-292 (2000)

The support code for these techniques is in MMTK.Subspace. An 
illustration can be found in Examples/NormalModes/mode_analysis.py.

Konrad.
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