A generalized parallel replica dynamics
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...
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| Published in | Journal of computational physics Vol. 284; no. C; pp. 595 - 616 |
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| Main Authors | , , |
| Format | Journal Article |
| Language | English |
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01.03.2015
Elsevier |
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| 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 with various numerical examples, including those with entropic barriers and the 2D Lennard-Jones cluster of seven atoms. |
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| AbstractList | 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 with various numerical examples, including those with entropic barriers and the 2D Lennard-Jones cluster of seven atoms. 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. |
| Author | Lelièvre, Tony Simpson, Gideon Binder, Andrew |
| Author_xml | – sequence: 1 givenname: Andrew surname: Binder fullname: Binder, Andrew – sequence: 2 givenname: Tony surname: Lelièvre fullname: Lelièvre, Tony – sequence: 3 givenname: Gideon surname: Simpson fullname: Simpson, Gideon email: simpson@math.drexel.edu |
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| Keywords | Quasi-stationary distributions Accelerated molecular dynamics Parallel replica dynamics Metastability |
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| Snippet | Metastability is a common obstacle to performing long molecular dynamics simulations. Many numerical methods have been proposed to overcome it. One method is... |
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| SubjectTerms | Accelerated molecular dynamics Algorithms Clusters Condensed Matter Convergence Diagnostic systems Dynamical systems Dynamics Materials Science Mathematics Metastability Molecular dynamics Numerical Analysis Parallel replica dynamics Physics Quasi-stationary distributions Stochastic processes |
| Title | A generalized parallel replica dynamics |
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