title: Efficient multiple time scale molecular dynamics: Using colored noise thermostats to stabilize resonances.
abstract: 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.
authors.affiliation: Department of Chemistry, Columbia University, New York, New York 10027, USA.
authors.forename: Joseph A
authors.initials: JA
authors.lastname: Morrone
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Markland
authors.forename: Michele
authors.initials: M
authors.lastname: Ceriotti
authors.forename: B J
authors.initials: BJ
authors.lastname: Berne
mesh_terms: D056004:Molecular Dynamics Simulation; D013696:Temperature; D013997:Time Factors