The Nose-Poincare method for constant temperature molecular dynamics

We present a new extended phase space method for constant temperature (canonical ensemble) molecular dynamics. Our starting point is the Hamiltonian introduced by Nose to generate trajectories corresponding to configurations in the canonical ensemble. Using a Poincare 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 (Nose-Hoover dynamics), which yields a time-reversible system but simultaneously destroys the Hamiltonian structure. A symplectic discretization method is presented for solving the Nose-Poincare 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 Nose chains, holonomic constraints, and rigid bodies, (C) 1999 Academic Press.