A molecular gas system in three dimensions is numerically studied by the energy conserving molecular dynamics (MD). The autocorrelation functions for the velocity and the force are computed and the friction coefficient is estimated. From the comparison with the stochastic dynamics (SD) of a Brownian particle, it is shown that the force correlation function in MD is different from the delta-function force correlation in SD in short time scale. However, as the measurement time scale is increased further, the ensemble equivalence between the microcanonical MD and the canonical SD is restored. We also discuss the practical implication of the result.