Journal of Chemical Physics, Vol.121, No.1, 108-116, 2004
The canonical ensemble via symplectic integrators using Nose and Nose-Poincare chains
Simulations that sample from the canonical ensemble can be generated by the addition of a single degree of freedom, provided that the system is ergodic, as described by Nose with subsequent modifications by Hoover to allow sampling in real time. Nose-Hoover dynamics is not ergodic for small or stiff systems and the addition of auxiliary thermostats is needed to overcome this deficiency. Nose-Hoover dynamics, like its derivatives, does not have a Hamiltonian structure, precluding the use of symplectic integrators which are noted for their long term stability and structure preservation. As an alternative to Nose-Hoover, the Hamiltonian Nose-Poincare method was proposed by Bond, Laird, and Leimkuhler [J. Comput. Phys. 151, 114 (1999)], but the straightforward addition of thermostatting chains does not sample from the canonical ensemble. In this paper a method is proposed whereby additional thermostats can be applied to a Hamiltonian system while retaining sampling from the canonical ensemble. This technique has been used to construct thermostatting chains for the Nose and Nose-Poincare methods. (C) 2004 American Institute of Physics.