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PubMed · 12069624

Long time dynamics of complex systems.

Ron Elber·Avijit Ghosh·Alfredo Cárdenas
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Abstract

Molecular dynamics trajectories of large biological molecules are restricted to nanoseconds. We describe a computational method, based on optimization of a functional, to extend the time of molecular simulations by orders of magnitude. Variants of our technique have already produced microsecond and millisecond trajectories. The large steps enable feasible computations of atomically detailed approximate trajectories. Numerical examples are provided: (i) a conformational change in blocked glycine peptide and (ii) helix formation of an alanine-rich peptide.

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Computer SimulationKineticsModels, ChemicalMotionPeptidesProtein Structure, SecondaryJournal ArticleResearch Support, U.S. Gov't, Non-P.H.S.Research Support, U.S. Gov't, P.H.S.Review

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BibTeXRIS

Ron Elber, Avijit Ghosh, Alfredo Cárdenas. 2002. Long time dynamics of complex systems.. https://doi.org/10.1021/ar010021d

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