[MMTK] Normal Modes

Konrad Hinsen konrad.hinsen at cea.fr
Fri Mar 24 18:42:06 CET 2006


On Mar 24, 2006, at 17:48, vanitha at cs.wisc.edu wrote:

> I am using an all-atom force field to do my minimization. And I  
> need to
> add the normal mode vector to the gradient of the energy (w.r.t.  
> cartesian
> co-rodinates of all atoms). I'd have vectors of differing lengths if I
> apply the normal mode calulation to just the C-Alpha model. I have to
> think about whether I can minimize the C-alpha model to begin with!

There are ways to extend a C-alpha mode vector to an all-atom  
displacement vector by interpolation. For example, you can create an  
AtomicVectorField from the C-alpha displacements and set the  
displacements of the all-atom model to the values of that field at  
the atom positions. That yields a spatial interpolation of the  
displacement vectors. Of course I cannot judge if this is a  
physically reasonable approach in your application.

Konrad.
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Konrad Hinsen
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