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Title: A generalized parallel replica dynamics

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Journal Article: Publisher's Accepted Manuscript
Journal Name:
Journal of Computational Physics
Additional Journal Information:
Journal Volume: 284; Journal Issue: C; Related Information: CHORUS Timestamp: 2017-07-04 09:24:21; Journal ID: ISSN 0021-9991
Country of Publication:
United States

Citation Formats

Binder, Andrew, Lelièvre, Tony, and Simpson, Gideon. A generalized parallel replica dynamics. United States: N. p., 2015. Web. doi:10.1016/
Binder, Andrew, Lelièvre, Tony, & Simpson, Gideon. A generalized parallel replica dynamics. United States. doi:10.1016/
Binder, Andrew, Lelièvre, Tony, and Simpson, Gideon. 2015. "A generalized parallel replica dynamics". United States. doi:10.1016/
title = {A generalized parallel replica dynamics},
author = {Binder, Andrew and Lelièvre, Tony and Simpson, Gideon},
abstractNote = {},
doi = {10.1016/},
journal = {Journal of Computational Physics},
number = C,
volume = 284,
place = {United States},
year = 2015,
month = 3

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record at 10.1016/

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Cited by: 8works
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Web of Science

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  • Metastability is a common obstacle to performing long molecular dynamics simulations. Many numerical methods have been proposed to overcome it. One method is parallel replica dynamics, which relies on the rapid convergence of the underlying stochastic process to a quasi-stationary distribution. Two requirements for applying parallel replica dynamics are knowledge of the time scale on which the process converges to the quasi-stationary distribution and a mechanism for generating samples from this distribution. By combining a Fleming–Viot particle system with convergence diagnostics to simultaneously identify when the process converges while also generating samples, we can address both points. This variation onmore » the algorithm is illustrated with various numerical examples, including those with entropic barriers and the 2D Lennard-Jones cluster of seven atoms.« less
  • Cited by 1
  • A prescription for sampling isobaric generalized ensembles with molecular dynamics is presented and applied to the generalized replica exchange method (gREM), which was designed for simulating first-order phase transitions. The properties of the isobaric gREM ensemble are discussed and a study is presented of the liquid-vapor equilibrium of the guest molecules given for gas hydrate formation with the mW water model. As a result, phase diagrams, critical parameters, and a law of corresponding states are obtained.
  • Although molecular-dynamics simulations can be parallelized effectively to treat large systems (10{sup 6}{endash}10{sup 8} atoms), to date the power of parallel computers has not been harnessed to make analogous gains in {ital time} scale. I present a simple approach for infrequent-event systems that extends the time scale with high parallel efficiency. Integrating a replica of the system independently on each processor until the first transition occurs gives the correct transition-time distribution, and hence the correct dynamics. I obtain {gt}90{percent} efficiency simulating Cu(100) surface vacancy diffusion on 15 processors. {copyright} {ital 1998} {ital The American Physical Society}
  • Protein and peptide aggregation into amyloid plaques is associated with a large variety of neurodegenerative diseases. The definition of the molecular bases of these pathologies is hampered by the transient nature of pre-fibrillar small-oligomers that are considered the toxic species. The ability of the peptide GNNQQNY to form amyloid-like structures makes it a good model to investigate the complex processes involved into amyloid fiber formation. By employing full atomistic replica exchange molecular dynamics simulations, we constructed the free energy surface of small assemblies of GNNQQNY to gain novel insights into the fiber formation process. The calculations suggest that the peptidemore » exhibits a remarkable tendency to form both parallel and antiparallel {beta}-sheets. The data show that GNNQQNY preference for parallel or antiparallel {beta}-sheets is governed by a subtle balance of factors including assemblies' size, sidechain-sidechain interactions and pH. The samplings analysis provides a rationale to the observed trends.« less