Displaying similar documents to “A Metropolis adjusted Nosé-Hoover thermostat”

Molecular Simulation in the Canonical Ensemble and Beyond

Zhidong Jia, Ben Leimkuhler (2007)

ESAIM: Mathematical Modelling and Numerical Analysis

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In this paper, we discuss advanced thermostatting techniques for sampling molecular systems in the canonical ensemble. We first survey work on dynamical thermostatting methods, including the Nosé-Poincaré method, and generalized bath methods which introduce a more complicated extended model to obtain better ergodicity. We describe a general controlled temperature model, () and demonstrate that it flexibly accommodates existing alternative thermostatting methods, such as Nosé-Poincaré,...

Theoretical and numerical comparison of some sampling methods for molecular dynamics

Eric Cancès, Frédéric Legoll, Gabriel Stoltz (2007)

ESAIM: Mathematical Modelling and Numerical Analysis

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The purpose of the present article is to compare different phase-space sampling methods, such as purely stochastic methods (Rejection method, Metropolized independence sampler, Importance Sampling), stochastically perturbed Molecular Dynamics methods (Hybrid Monte Carlo, Langevin Dynamics, Biased Random Walk), and purely deterministic methods (Nosé-Hoover chains, Nosé-Poincaré and Recursive Multiple Thermostats (RMT) methods). After recalling some theoretical convergence properties...

Combining stochastic and deterministic approaches within high efficiency molecular simulations

Bruno Escribano, Elena Akhmatskaya, Jon Mujika (2013)

Open Mathematics

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Generalized Shadow Hybrid Monte Carlo (GSHMC) is a method for molecular simulations that rigorously alternates Monte Carlo sampling from a canonical ensemble with integration of trajectories using Molecular Dynamics (MD). While conventional hybrid Monte Carlo methods completely re-sample particle’s velocities between MD trajectories, our method suggests a partial velocity update procedure which keeps a part of the dynamic information throughout the simulation. We use shadow (modified)...