Cargando…

Time Step Rescaling Recovers Continuous-Time Dynamical Properties for Discrete-Time Langevin Integration of Nonequilibrium Systems

[Image: see text] When simulating molecular systems using deterministic equations of motion (e.g., Newtonian dynamics), such equations are generally numerically integrated according to a well-developed set of algorithms that share commonly agreed-upon desirable properties. However, for stochastic eq...

Descripción completa

Detalles Bibliográficos
Autores principales: Sivak, David A., Chodera, John D., Crooks, Gavin E.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2014
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4065221/
https://www.ncbi.nlm.nih.gov/pubmed/24555448
http://dx.doi.org/10.1021/jp411770f
_version_ 1782322044038283264
author Sivak, David A.
Chodera, John D.
Crooks, Gavin E.
author_facet Sivak, David A.
Chodera, John D.
Crooks, Gavin E.
author_sort Sivak, David A.
collection PubMed
description [Image: see text] When simulating molecular systems using deterministic equations of motion (e.g., Newtonian dynamics), such equations are generally numerically integrated according to a well-developed set of algorithms that share commonly agreed-upon desirable properties. However, for stochastic equations of motion (e.g., Langevin dynamics), there is still broad disagreement over which integration algorithms are most appropriate. While multiple desiderata have been proposed throughout the literature, consensus on which criteria are important is absent, and no published integration scheme satisfies all desiderata simultaneously. Additional nontrivial complications stem from simulating systems driven out of equilibrium using existing stochastic integration schemes in conjunction with recently developed nonequilibrium fluctuation theorems. Here, we examine a family of discrete time integration schemes for Langevin dynamics, assessing how each member satisfies a variety of desiderata that have been enumerated in prior efforts to construct suitable Langevin integrators. We show that the incorporation of a novel time step rescaling in the deterministic updates of position and velocity can correct a number of dynamical defects in these integrators. Finally, we identify a particular splitting (related to the velocity Verlet discretization) that has essentially universally appropriate properties for the simulation of Langevin dynamics for molecular systems in equilibrium, nonequilibrium, and path sampling contexts.
format Online
Article
Text
id pubmed-4065221
institution National Center for Biotechnology Information
language English
publishDate 2014
publisher American Chemical Society
record_format MEDLINE/PubMed
spelling pubmed-40652212015-02-20 Time Step Rescaling Recovers Continuous-Time Dynamical Properties for Discrete-Time Langevin Integration of Nonequilibrium Systems Sivak, David A. Chodera, John D. Crooks, Gavin E. J Phys Chem B [Image: see text] When simulating molecular systems using deterministic equations of motion (e.g., Newtonian dynamics), such equations are generally numerically integrated according to a well-developed set of algorithms that share commonly agreed-upon desirable properties. However, for stochastic equations of motion (e.g., Langevin dynamics), there is still broad disagreement over which integration algorithms are most appropriate. While multiple desiderata have been proposed throughout the literature, consensus on which criteria are important is absent, and no published integration scheme satisfies all desiderata simultaneously. Additional nontrivial complications stem from simulating systems driven out of equilibrium using existing stochastic integration schemes in conjunction with recently developed nonequilibrium fluctuation theorems. Here, we examine a family of discrete time integration schemes for Langevin dynamics, assessing how each member satisfies a variety of desiderata that have been enumerated in prior efforts to construct suitable Langevin integrators. We show that the incorporation of a novel time step rescaling in the deterministic updates of position and velocity can correct a number of dynamical defects in these integrators. Finally, we identify a particular splitting (related to the velocity Verlet discretization) that has essentially universally appropriate properties for the simulation of Langevin dynamics for molecular systems in equilibrium, nonequilibrium, and path sampling contexts. American Chemical Society 2014-02-20 2014-06-19 /pmc/articles/PMC4065221/ /pubmed/24555448 http://dx.doi.org/10.1021/jp411770f Text en Copyright © 2014 American Chemical Society Open Access on 02/20/2015
spellingShingle Sivak, David A.
Chodera, John D.
Crooks, Gavin E.
Time Step Rescaling Recovers Continuous-Time Dynamical Properties for Discrete-Time Langevin Integration of Nonequilibrium Systems
title Time Step Rescaling Recovers Continuous-Time Dynamical Properties for Discrete-Time Langevin Integration of Nonequilibrium Systems
title_full Time Step Rescaling Recovers Continuous-Time Dynamical Properties for Discrete-Time Langevin Integration of Nonequilibrium Systems
title_fullStr Time Step Rescaling Recovers Continuous-Time Dynamical Properties for Discrete-Time Langevin Integration of Nonequilibrium Systems
title_full_unstemmed Time Step Rescaling Recovers Continuous-Time Dynamical Properties for Discrete-Time Langevin Integration of Nonequilibrium Systems
title_short Time Step Rescaling Recovers Continuous-Time Dynamical Properties for Discrete-Time Langevin Integration of Nonequilibrium Systems
title_sort time step rescaling recovers continuous-time dynamical properties for discrete-time langevin integration of nonequilibrium systems
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4065221/
https://www.ncbi.nlm.nih.gov/pubmed/24555448
http://dx.doi.org/10.1021/jp411770f
work_keys_str_mv AT sivakdavida timesteprescalingrecoverscontinuoustimedynamicalpropertiesfordiscretetimelangevinintegrationofnonequilibriumsystems
AT choderajohnd timesteprescalingrecoverscontinuoustimedynamicalpropertiesfordiscretetimelangevinintegrationofnonequilibriumsystems
AT crooksgavine timesteprescalingrecoverscontinuoustimedynamicalpropertiesfordiscretetimelangevinintegrationofnonequilibriumsystems