It is shown that a principal component analysis of a large set of internal coordinates can be used to deﬁne a nonredundant set of delocalized internal coordinates suitable for the calculation of harmonic vibrational normal modes. The selection of internal coordinates and the principal component analysis provide large degrees of freedom in extracting a nonredundant set of coordinates, and thus inﬂuence how the vibrational normal modes are described. It is shown that long-range coordinates may be especially suitable for describing low-frequency global deformation modes in proteins.
- vibrational analysis
- internal coordinates