  It has been reported recently that the equipartition theorem is violated in
molecular dynamics simulations with periodic boundary condition [Shirts et al,
J. Chem. Phys. 125, 164102 (2006)]. This effect is associated with the
conservation of the center of mass momentum. Here, we propose a fluctuating
center of mass molecular dynamics approach (FCMMD) to solve this problem. Using
the analogy to a system exchanging momentum with its surroundings, we work out
--and validate via simulations-- an expression for the rate at which
fluctuations shall be added to the system. The restoration of equipartition
within the FCMMD is then shown both at equilibrium as well as beyond
equilibrium in the linear response regime.
