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Multiple time scale molecular dynamics enhances computational efficiency byupdating slow motions less frequently than fast motions. However, in practicethe largest outer time step possible is limited not by the physical forces butby resonances between the fast and slow modes. In this paper we show that thisproblem can be alleviated by using a simple colored noise thermostatting schemewhich selectively targets the high frequency modes in the system. For twosample problems, flexible water and solvated alanine dipeptide, we demonstratethat this allows the use of large outer time steps while still obtainingaccurate sampling and minimizing the perturbation of the dynamics. Furthermore,this approach is shown to be comparable to constraining fast motions, thusproviding an alternative to molecular dynamics with constraints.

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