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We consider the problem of how a condensed molecular system approaches equilibrium, focusing on the particular case of water. We show, by means of extensive molecular dynamics simulations, that the existence of different types of degrees of freedom affects the dynamics of equilibration, and this influence is made most obvious in the system's temperature. When equipartition of energy does not hold in the initial, nonequilibrium state, the instantaneous temperature can be up to a few degrees lower than that observed under equipartition conditions, resulting in a Mpemba-like effect. Though our study considers water in particular, our findings apply more generally to condensed molecular systems.