[MMTK] question about modes

khinsen at cea.fr khinsen at cea.fr
Mon Jul 18 17:04:03 CEST 2005


On Jul 15, 2005, at 1:46, OMAR NABEEL ALY DEMERDASH wrote:

> Dear sir or madam,
> Of course, in normal mode analysis MMTK undoes the mass-weighting of
> the eigenvectors, rendering them not orthonormal.  Therefore, would one
> simply transform a matrix V consisting of these non orthonormal vectors
> to recover the original orthonormal eigenvectors like so:
>
> M^(-1/2)*V*M^(-1/2) ?

Yes.

> Moreover, would the masses in M simply be the masses of the residues in
> the order in which they occur in the PDB file?

No, not necessarily. However, the order of the atoms can always be 
identified by looking at atom.index, i.e. M[atom.index] is the mass of 
the particle "atom".

In general, it is strongly discouraged to refer to atom indices or atom 
order explicitly in Python code using MMTK. It is never necessary 
except where data must be imported from or exported to the "outer 
world", i.e. outside of MMTK objects.

> Finally, when converting the modes that result from use of the fourier
> basis to orthonormal eigenvectors, is there any other transformation
> other than mass-weighting that needs to occur?

No. The use of a restricted subspace (such as a FourierBasis) still 
yields orthonormal modes (up to mass weighting), but the set of all 
modes is no longer a basis for the full Cartesian coordinate space, 
only for the subspace being used.

Konrad.
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Konrad Hinsen
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E-Mail: khinsen at cea.fr
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