Variational Approach to Molecular Kinetics

Feliks Nueske, Bettina G. Keller*, Guillermo Perez-Hernandez, Antonia S. J. S. Mey, Frank Noe

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

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 to 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.

Original languageEnglish
Pages (from-to)1739-1752
Number of pages14
JournalJournal of Chemical Theory and Computation
Volume10
Issue number4
DOIs
Publication statusPublished - Apr 2014

Keywords

  • DYNAMICS SIMULATIONS
  • STATE MODELS
  • CONFORMATIONAL DYNAMICS
  • TRANSITION NETWORKS
  • HIDDEN COMPLEXITY
  • FOLDING PATHWAYS
  • MARKOV-MODELS
  • PROTEINS
  • TRAJECTORIES
  • FINGERPRINTS

Cite this