Temperature fluctuations in canonical systems: Insights from molecular   dynamics simulations
  Molecular dynamics simulations of a quasi-harmonic solid are conducted to elucidate the meaning of temperature fluctuations in canonical systems and validate a well-known but frequently contested equation predicting the mean square of such fluctuations. The simulations implement two virtual and one physical (natural) thermostat and examine the kinetic, potential and total energy correlation functions in the time and frequency domains. The results clearly demonstrate the existence of quasi-equilibrium states in which the system can be characterized by a well-defined temperature that follows the mentioned fluctuation equation. The emergence of such states is due to the wide separation of timescales between thermal relaxation by phonon scattering and slow energy exchanges with the thermostat. The quasi-equilibrium states exist between these two timescales when the system behaves as virtually isolated and equilibrium. 
J. Hickman and Y. Mishin
cond-mat.stat-mech