  The average kinetic energy is widely used to characterize temperature in
molecular dynamics (MD) simulation. In this letter, the applicability of three
types of average kinetic energy as measures of temperature is investigated,
i.e., the total kinetic energy, kinetic energy without the centroid translation
part, and thermal disturbance kinetic energy. Our MD simulations indicate that
definitions of temperature based on the kinetic energy including rigid
translational or rotational motion may yield unrealistic results. In contrast,
the thermal disturbance kinetic energy has wider applicability to temperature
computation in non-equilibrium molecular dynamics simulation. If small samples
need to be used for local temperature, then a calibration approach is proposed
to eliminate the sample-size dependence of the average disturbance kinetic
energy.
