Discrete Newtonian dynamics with Nosé-Hoover thermostats (2403.01612v1)

Abstract: Almost all Molecular Dynamics (MD) simulations are discrete dynamics with Newton's algorithm first published in 1687, and much later by L. Verlet in 1967. Discrete Newtonian dynamics has the same qualities as Newton's classical analytic dynamics. Verlet also published a first-order expression for the instant temperature which is inaccurate but presumably used in most MD simulations. One of the motivations for the present article is to correct this unnecessary inaccuracy in $NVT$ MD dynamics. Another motivation is to derive simple algorithms for the Nos\'{e}-Hoover $NVT$ dynamics (NH) with the correct temperature constraint. The simulations with NH discrete Newtonian dynamics show that the NH works excellent for a wide range of the response time $\tau$ of the NH thermostat, but NH simulations favor a choice of a short response time, even shorter than the discrete-time increment $\delta t$ used in MD, to avoid large oscillations of the temperature.