Efficient multiple time scale molecular dynamics: using colored noise thermostats to stabilize resonances

Multiple time scale molecular dynamics enhances computational efficiency by updating slow motions less frequently than fast motions. However, in practice the largest outer time step possible is limited not by the physical forces but by resonances between the fast and slow modes. In this paper we show that this problem can be alleviated by using a simple colored noise thermostatting scheme which selectively targets the high frequency modes in the system. For two sample problems, flexible water and solvated alanine dipeptide, we demonstrate that this allows the use of large outer time steps while still obtaining accurate sampling and minimizing the perturbation of the dynamics. Furthermore, this approach is shown to be comparable to constraining fast motions, thus providing an alternative to molecular dynamics with constraints.Comment: accepted for publication by the Journal of Chemical Physic

Mode-coupling theory for reaction dynamics in liquids

A theory for chemical reaction dynamics in condensed phase systems based on the generalized Langevin formalism of Grote and Hynes is presented. A microscopic approach to calculate the dynamic friction is developed within the framework of a combination of kinetic and mode-coupling theories. The approach provides a powerful analytic tool to study chemical reactions in realistic condensed phase environments. The accuracy of the approach is tested for a model isomerization reaction in a Lennard-Jones fluid. Good agreement is obtained for the transmission coefficient at different solvent densities, in comparison with numerical simulations based on the reactive-flux approach.Comment: 7 pages, 3 figure