Variational Approach to Molecular Kinetics
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- 作者：Feliks N眉ske ; Bettina G. Keller ; Guillermo P茅rez-Hern谩ndez ; Antonia S. J. S. Mey ; Frank No茅
- 刊名：Journal of Chemical Theory and Computation
- 出版年：2014
- 出版时间：April 8, 2014
- 年：2014
- 卷：10
- 期：4
- 页码：1739-1752
- 全文大小：640K
- 年卷期：v.10,no.4(April 8, 2014)
- ISSN：1549-9626
文摘
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.