Normal mode analysis (NMA) is a mathematical method that can be used to predict the local dynamics of macromolecules. It relies on the harmonic approximation, which assumes that the starting structure occupies a physiologically relevant energy minimum. Normal modes are derived by diagonalization of a matrix describing the second derivative of the potential energy surface, yielding eigenvalues corresponding to vibrational frequencies and eigenvectors corresponding to the modes. Typically only the lowest-frequency modes are of interest.
Implementations
- Rosetta NormalModeRelax
- ProDy (http://www.bahargroup.org/prody/)
- elNémo (https://www.sciences.univ-nantes.fr/elnemo/)