E. Barth, B. Leimkuhler, C.R. Sweet

The evaluation of molecular dynamics models incorporating temperature control methods is of great importance for molecular dynamics practitioners. In this paper, we study the way in which biomolecular systems achieve thermal equilibrium. In unthermostatted (constant energy) and Nose-Hoover dynamics simulations, correct partition of energy is not observed on a typical MD simulation timescale. We discuss the practical use of numerical schemes based on Nose-Hoover chains, Nose-Poincare and recursive multiple thermostats (RMT) [8], with particular reference to parameter selection, and show that RMT appears to show the most promise as a method for correct thermostatting. All of the MD simulations were carried out using a variation of the CHARMM package in which the Nose-Poincare, Nose-Hoover Chains and RMT methods have been implemented.