  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.
