konrad.hinsen@cea.fr konrad.hinsen at cea.fr
Tue Mar 14 12:02:45 CET 2006

On 10.03.2006, at 13:58, vanitha at cs.wisc.edu wrote:

> I see that one can do a sparse matrix normal mode analysis within  
> MMTK. Is
> the Implicitly Restarted Arnoldi method (ARPACK) being used to  
> compute the
> normal modes in this case. Also, what model does the NMA code in  
> MMTK use?
> Elastic Network Model or a Force-field based one?

An Elastic Network Model is nothing else but a particular choice of  
force field. MMTK contains two Elastic Network force fields  
(DeformationForceField and CalphaForceField) and one all-atom force  
field (Amber94ForceField), which can all be used for normal mode  

As for the use of sparse matrices, note that you need to install the  
add-on module MMTK_SparseModes, which contains ARPACK code plus an  
interface module. The reason for keeping this separate is that the  
ARPACK licensing conditions are not clear to me. I prefer to stay  
away from legal trouble.

Without this add-on module, you can still use sparse matrices in  
combination with an explicit basis. In that case, the Hessian for the  
given basis is calculated from a sparse all-atom Hessian, and  
diagonalized as usual. If the basis is much smaller than the all-atom  
basis, and the force field has a small effective cutoff, this uses  
much less memory than the standard approach.

Konrad Hinsen
Laboratoire Leon Brillouin (CEA-CNRS), CEA Saclay,
91191 Gif-sur-Yvette Cedex, France
Tel.: +33-1 69 08 79 25
Fax: +33-1 69 08 82 61
E-Mail: konrad.hinsen at cea.fr

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