F. Nüske, B.G. Keller, G. Perez-Hernnandez, A.S.J.S. Mey, F. Noé— 2014
The eigenvalues and eigenvectors of the molecular dynamics propagator (or transfer operator) contain the essential information about the molecular thermodynamics and kinetics. This includes the stationary distribution, the metastable states, and state-to-state transition rates. Here we present a variational approach for computing these dominant eigenvalues and eigenvectors. This approach is analogous the variational approach used for computing stationary states in quantum mechanics. A corresponding method of linear variation is formulated. It is shown that the matrices needed for the linear variation method are correlation matrices that can be estimated from simple MD simulations for a given basis set. The method proposed here is thus, to first define a basis set able to capture the relevant conformational transitions, then compute the respective correlation matrices, and then to compute their dominant eigenvalues and eigenvectors, thus obtaining the key ingredients of the slow kinetics.
Variational approach to molecular kinetics
F. Nüske, B.G. Keller, G. Perez-Hernnandez, A.S.J.S. Mey, F. Noé