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Journal article
A generalized parallel replica dynamics
Journal of computational physics, v 284(C), pp 595-616
Mar 2015
Abstract
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 on the algorithm is illustrated on various numerical examples, including those with entropic barriers and the 2D Lennard-Jones cluster of seven atoms.
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Details
- Title
- A generalized parallel replica dynamics
- Creators
- Andrew J. Binder - University of Minnesota‐Twin CitiesTony Lelièvre - Center for Training and Research in MathematIcs and Scientific ComputingGideon Simpson - Drexel University
- Publication Details
- Journal of computational physics, v 284(C), pp 595-616
- Publisher
- Elsevier
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Mathematics
- Web of Science ID
- WOS:000348756700029
- Scopus ID
- 2-s2.0-84921503478
- Other Identifier
- 991019297099804721
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- Web of Science research areas
- Computer Science, Interdisciplinary Applications
- Physics, Mathematical