[MMTK] question about modes
OMAR NABEEL ALY DEMERDASH
ondemerdash at wisc.edu
Fri Jul 15 01:46:56 CEST 2005
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:
Moreover, would the masses in M simply be the masses of the residues in
the order in which they occur in the PDB file?
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?
Help is greatly appreciated!
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