Hamiltonian thermostatting techniques for molecular dynamics simulation
Molecular dynamics trajectories that sample from a Gibbs, or canonical, distribution can be generated by introducing a modified Hamiltonian with additional degrees of freedom as described by Nose . Although this method has found widespread use in its time re-parameterized Nose-Hoover form, the lack of a Hamiltonian, and the need to 'tune' thermostatting parameters has limited, its use compared to stochastic methods. In addition, since the proof of the correct sampling is based on an ergodic assumption, thermostatting small of stiff systems often does not given the correct distributions unless the Nose-Hoover chains  method is used, which inherits the Nose-Hoover deficiencies noted above. More recently the introduction of the Hamiltonian Nose-Poincare method , where symplectic integrators can be used for improved long term stability, has renewed interest in the possibility of Hamiltonian methods which can improve dynamical sampling. This class of methods, although applicable to small systems, has applications in large scale systems with complex chemical structure, such as protein-bath and quantum-classical models.;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. By the introduction of multiple thermostat Hamiltonian formulations, which are not restricted to chains, it has been possible to clarify this perspective, using harmonic models, and exhibit practical deficiencies of the standard Nose-chain approach. This has led to the introduction of two Hamiltonian schemes, the Nose-Poincare chains method and the Recursive Multiple Thermostat (RMT) method. The RMT method obtains canonical sampling without the stability problems encountered with chains with the advantage that the choice of Nose mass is independent of the underlying system.