Smart resolution replica exchange: an efficient algorithm for exploring complex energy landscapes.

Smart resolution replica exchange: an efficient algorithm for exploring complex energy landscapes. Research Abstract Details 

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Smart resolution replica exchange: an efficient algorithm for exploring complex energy landscapes. Abstract Text:

Pu Liu,Gregory A Voth,

A coarse-grained representation of a condensed phase system can significantly reduce the number of system degrees of freedom, making coarse-grained simulations very computationally efficient. Moreover, coarse graining can smoothen the free energy landscape of the system. Thus coarse-grained dynamics is usually faster than its fully atomistic counterpart. In this work, the smart resolution replica exchange method is introduced that incorporates the information from coarse-grained simulations into atomistic simulations in order to accelerate the sampling of rough, complex atomistic energy landscapes. Within this methodology, interactions between particles are defined by a potential energy that interpolates between a fully atomistic potential and a fully coarse-grained effective potential according to a parameter lambda. Instead of exchanging the configurations from neighboring resolutions directly, as has been done in the resolution replica exchange methods [E. Lyman et al., Phys. Rev. Lett. 96, 028105 (2006); M. Christen and W. F. v. Gunsteren, J. Chem. Phys. 124, 154106 (2006)], the configuration described at the coarser resolution is first relaxed before an exchange is attempted, similar to the smart walking method [R. Zhou and B. J. Berne, J. Chem. Phys. 107, 9185 (1997)]. This approach greatly increases the acceptance ratio of exchange and only two replicas, one at the atomistic level and one at the coarse-grained level, are usually required (although more can be implemented if desired). This new method can approximately obtain the correct canonical sampling if the exchange interval is sufficiently large to allow the system to explore the local energy landscape. The method is demonstrated for a two-dimensional model system, where the ideal population distribution can be recovered, and also for an alanine polypeptide (Ala(15)) model with explicit water, where its native structure, an alpha helix, is obtained from the extended structure within 1 ns.

Smart resolution replica exchange: an efficient algorithm for exploring complex energy landscapes. Publishing Authors By Initials

P Liu,GA Voth,

For similar natural sciences: science: models, theoretical: models, molecular research abstracts see: natural sciences: science: models, theoretical: models, molecular research

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Smart resolution replica exchange: an efficient algorithm for exploring complex energy landscapes. Journal Published:

PUBLICATION TYPE: Research Support, U.S. Gov't,

Journal: The Journal of chemical physics

VOLUME: 126

Page Numbers: 045106

Journal Abbreviation:

ISSN: 0021-9606

DAY: 28

MONTH: Jan

YEAR: 2007

Smart resolution replica exchange: an efficient algorithm for exploring complex energy landscapes. Information

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LANGUAGE: eng

NlmUniqueID: 375360

Smart resolution replica exchange: an efficient algorithm for exploring complex energy landscapes. Keywords Mesh Terms:

KEYWORDS: Models, Molecular

MESH TERMS: chemistry

Chemical & Substance for Abstract: Smart resolution replica exchange: an efficient algorithm for exploring complex energy landscapes. Information

Substance Name: Biopolymers

Registry Number: 0

Grant and Affiliation Information for Smart resolution replica exchange: an efficient algorithm for exploring complex energy landscapes.

AFFILIATION: Center for Biophysical Modeling and Simulation, University of Utah, Salt Lake City, Utah 84112-0850, USA.

Country: United States

AGENCY: United States NIGMS

GRANT: GM63796

ACRONYM: GM

MEDLINETA: J Chem Phys

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