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Stephen D. Bond

Citation:

Stephen D. Bond, Benedict J. Leimkuhler and Brian B. Laird, The Nosé-Poincaré Method for Constant Temperature Molecular Dynamics, Journal of Computational Physics 151 (1999) 114-134.

Abstract:

We present a new extended phase space method for constant temperature (canonical ensemble) molecular dynamics. Our starting point is the Hamiltonian introduced by Nosé to generate trajectories corresponding to configurations in the canonical ensemble. Using a Poincaré time-transformation, we construct a Hamiltonian system with the correct intrinsic timescale and show that it generates trajectories in the canonical ensemble. Our approach corrects a serious deficiency of the standard change of variables (Nosé-Hoover dynamics), which yields a time-reversible system but simultaneously destroys the Hamiltonian structure. A symplectic discretization method is presented for solving the Nosé-Poincaré equations. The method is explicit and preserves the time-reversal symmetry. In numerical experiments, it is shown that the new method exhibits enhanced stability when the temperature fluctuation is large. Extensions are presented for Nosé chains, holonomic constraints, and rigid bodies.

Full Text:

DOI: 10.1006/jcph.1998.6171

Preprint:

The Nosé-Poincaré Method for Constant Temperature Molecular Dynamics (400K, PDF)

Bibtex:
@article{BLL1999,
  author  = {Stephen D. Bond and Benedict J. Leimkuhler and Brian B. Laird},
  title   = {The Nos\'e-Poincar\'e Method for Constant Temperature Molecular
             Dynamics},
  journal = {Journal of Computational Physics},
  volume  = 151,
  year    = 1999,
  pages   = {114--134},
  doi     = {10.1006/jcph.1998.6171}
}

Stephen Bond