The behaviour of the total momentum of a system immersed in the Berendsen thermostat is analyzed. It has been found that under certain conditions the kinetic energy of the system can be transformed from internal degrees of freedom to the external ones, and conversely. A concrete example of such a transformation is presented. The results of molecular dynamics simulations of the Fe₄S₄(SH)₄ complex coupled to different external heat baths are discussed.

This paper presents an analytical investigation for the velocity relaxation of a test particle coupled to a heat bath by two different mechanisms: the Brownian dynamics (BD) and the collisional dynamics (CD). Relation between the parameters of the methods is established. The velocity relaxation spectrum induced by the coupling in the CD method is shown to be different from the one in the BD method. The difference between the spectra disappears in the limit γ → O, where γ is a mass ratio of the bath atoms and the test particle.