Journal
SIAM JOURNAL ON APPLIED DYNAMICAL SYSTEMS
Volume 4, Issue 1, Pages 187-216Publisher
SIAM PUBLICATIONS
DOI: 10.1137/040606090
Keywords
Nose; Nose-Hoover; Nose-Poincare; Nose-Poincare chains; symplectic integrator; constant temperature molecular dynamics; thermostatting
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Molecular dynamics trajectories that sample from a Gibbs distribution can be generated by introducing a modified Hamiltonian with additional degrees of freedom as described by Nose [S. Nose, Mol. Phys., 52 ( 1984), p. 255]. To achieve the ergodicity required for canonical sampling, a number of techniques have been proposed based on incorporating additional thermostatting variables, such as Nose - Hoover chains and more recent fully Hamiltonian generalizations. For Nose dynamics, it is often stated that the system is driven to equilibrium through a resonant interaction between the self-oscillation frequency of the thermostat variable and a natural frequency of the underlying system. In this article, we clarify this perspective, using harmonic models, and exhibit practical deficiencies of the standard Nose chain approach. As a consequence of our analysis, we propose a new powerful recursive thermostatting procedure which obtains canonical sampling without the stability problems encountered with Nose - Hoover and Nose - Poincare chains.
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