Committor-Consistent Variational String Method.


Journal

The journal of physical chemistry letters
ISSN: 1948-7185
Titre abrégé: J Phys Chem Lett
Pays: United States
ID NLM: 101526034

Informations de publication

Date de publication:
13 Oct 2022
Historique:
pubmed: 30 9 2022
medline: 15 10 2022
entrez: 29 9 2022
Statut: ppublish

Résumé

The treatment of slow and rare transitions in the simulation of complex systems poses a great computational challenge. A powerful approach to tackle this challenge is the string method, which represents the transition path as a one-dimensional curve in a multidimensional space of collective variables. Commonly used strategies for pathway optimization include aligning the tangent of the string to the local mean force or to the mean drift determined from swarms of short trajectories. Here, a novel strategy is proposed, allowing the string to be optimized based on a variational principle involving the unidirectional reactive flux expressed in terms of the time-correlation function of the committor. The method is illustrated with model systems and then probed with the alanine dipeptide and a coarse-grained model of the barstar-barnase protein complex. Successive iterations variationally refine the string toward an optimal transition pathway following the gradient of the committor between two metastable states.

Identifiants

pubmed: 36173307
doi: 10.1021/acs.jpclett.2c02529
doi:

Substances chimiques

Dipeptides 0
Alanine OF5P57N2ZX

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

9263-9271

Auteurs

Ziwei He (Z)

Department of Chemistry, The University of Chicago, 5735 S. Ellis Avenue, Chicago60637, Illinois, United States.

Christophe Chipot (C)

Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche No. 7019, Université de Lorraine, B.P. 70239, Vandœuvre-lès-Nancy cedex54506, France.

Benoît Roux (B)

Department of Chemistry, The University of Chicago, 5735 S. Ellis Avenue, Chicago60637, Illinois, United States.
Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago60637, IllinoisUnited States.

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Classifications MeSH