Variational Approach to Molecular Kinetics.
J Chem Theory Comput
; 10(4): 1739-52, 2014 Apr 08.
Article
em En
| MEDLINE
| ID: mdl-26580382
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.
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Coleções:
01-internacional
Base de dados:
MEDLINE
Idioma:
En
Revista:
J Chem Theory Comput
Ano de publicação:
2014
Tipo de documento:
Article
País de afiliação:
Alemanha