Local Resampling Trick for Focused Molecular Dynamics.

Fass, Joshua; York, Forrest; Wittmann, Matthew; Kaus, Joseph; Zhao, Yutong

Fass, Joshua; York, Forrest; Wittmann, Matthew; Kaus, Joseph; Zhao, Yutong.

Afiliación

Fass J; Computation, Relay Therapeutics, Cambridge, Massachusetts 02139, United States.
York F; Computation, Relay Therapeutics, Cambridge, Massachusetts 02139, United States.
Wittmann M; Computation, Relay Therapeutics, Cambridge, Massachusetts 02139, United States.
Kaus J; Computation, Relay Therapeutics, Cambridge, Massachusetts 02139, United States.
Zhao Y; Computation, Relay Therapeutics, Cambridge, Massachusetts 02139, United States.

J Chem Theory Comput ; 19(18): 6139-6150, 2023 Sep 26.

Article en En | MEDLINE | ID: mdl-37706456

RESUMEN

We describe a method that focuses sampling effort on a user-defined selection of a large system, which can lead to substantial decreases in computational effort by speeding up the calculation of nonbonded interactions. A naive approach can lead to incorrect sampling if the selection depends on the configuration in a way that is not accounted for. We avoid this pitfall by introducing appropriate auxiliary variables. This results in an implementation that is closely related to "configurational freezing" and "elastic barrier dynamical freezing." We implement the method and validate that it can be used to supplement conventional molecular dynamics in free energy calculations (absolute hydration and relative binding).

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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: J Chem Theory Comput Año: 2023 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Estados Unidos

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