A generalized parallel replica dynamics
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Publication:729033
DOI10.1016/J.JCP.2015.01.002zbMATH Open1352.92187arXiv1404.6191OpenAlexW2018595752MaRDI QIDQ729033FDOQ729033
Authors: Andrew Binder, Gideon Simpson, Tony Lelièvre 
Publication date: 20 December 2016
Published in: Journal of Computational Physics (Search for Journal in Brave)
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.
Full work available at URL: https://arxiv.org/abs/1404.6191
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Biochemistry, molecular biology (92C40) Chemistry (92E99) Computational methods for problems pertaining to biology (92-08)
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Cited In (16)
- Stationary Averaging for Multiscale Continuous Time Markov Chains Using Parallel Replica Dynamics
- Deterministic replica-exchange method without pseudo random numbers for simulations of complex systems
- Quasi-stationary distribution for strongly Feller Markov processes by Lyapunov functions and applications to hypoelliptic Hamiltonian systems
- Generalizing Parallel Replica Dynamics: Trajectory Fragments, Asynchronous Computing, and PDMPs
- Local and global perspectives on diffusion maps in the analysis of molecular systems
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- Numerical analysis of parallel replica dynamics
- Title not available (Why is that?)
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- A mathematical formalization of the parallel replica dynamics
- The parallel replica method for simulating long trajectories of Markov chains
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