Theoretical and numerical comparison of some sampling methods for
 molecular dynamics

Eric Cancès; Frédéric Legoll; Gabriel Stoltz

Displaying similar documents to “Theoretical and numerical comparison of some sampling methods for molecular dynamics”

A Metropolis adjusted Nosé-Hoover thermostat

Benedict Leimkuhler, Sebastian Reich (2009)

ESAIM: Mathematical Modelling and Numerical Analysis

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We present a Monte Carlo technique for sampling from the canonical distribution in molecular dynamics. The method is built upon the Nosé-Hoover constant temperature formulation and the generalized hybrid Monte Carlo method. In contrast to standard hybrid Monte Carlo methods only the thermostat degree of freedom is stochastically resampled during a Monte Carlo step.

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)...

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,...