A generalized parallel replica dynamics

DOI10.1016/J.JCP.2015.01.002zbMATH Open1352.92187OpenAlexW2018595752MaRDI QIDQ729033FDOQ729033

Authors Andrew Binder, Gideon Simpson, Tony Lelièvre 

Publication date 20 December 2016

Published in Journal of Computational Physics (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1404.6191

zbMATH Keywords

metastabilityquasi-stationary distributionsaccelerated molecular dynamicsparallel replica dynamics

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Chemistry (92E99) Computational methods for problems pertaining to biology (92-08)

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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Cited in

(16)

• Partial differential equations and stochastic methods in molecular dynamics
• Accelerated causal Green's function molecular dynamics
• Numerical analysis of parallel replica dynamics
• Sharp asymptotics of the first exit point density
• scientific article; zbMATH DE number 2226625 (Why is no real title available?)
• Analysis of the accelerated weighted ensemble methodology
• The parallel replica method for computing equilibrium averages of Markov chains
• Deterministic replica-exchange method without pseudo random numbers for simulations of complex systems
• Local and global perspectives on diffusion maps in the analysis of molecular systems
• A mathematical formalization of the parallel replica dynamics
• Stationary Averaging for Multiscale Continuous Time Markov Chains Using Parallel Replica Dynamics
• Quasi-stationary distribution for strongly Feller Markov processes by Lyapunov functions and applications to hypoelliptic Hamiltonian systems
• The enhanced sampling in parallel finite-time dynamics method with replica exchange
• Adaptive multilevel splitting in molecular dynamics simulations
• Generalizing Parallel Replica Dynamics: Trajectory Fragments, Asynchronous Computing, and PDMPs
• The parallel replica method for simulating long trajectories of Markov chains

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Uses Software

• SPRNG
• GSL

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