The thermodynamic behaviour of self-gravitating $N$-body systems has been worked out by borrowing a standard method from Molecular Dynamics: the time averages of suitable quantities are numerically computed along the dynamical trajectories to yield thermodynamic observables. The link between dynamics and thermodynamics is made in the microcanonical ensemble of statistical mechanics. The dynamics of self-gravitating $N$-body systems has been computed using two different kinds of regularization of the newtonian interaction: the usual softening and a truncation of the Fourier expansion series of the two-body potential. $N$ particles of equal masses are constrained in a finite three dimensional volume. Through the computation of basic thermodynamic observables and of the equation of state in the $P - V$ plane, new evidence is given of the existence of a second order phase transition from a homogeneous phase to a clustered phase. This corresponds to a crossover from a polytrope of index $n=3$, i.e. $p=K V^{-4/3}$, to a perfect gas law $p=K V^{-1}$, as is shown by the isoenergetic curves on the $P - V$ plane. The dynamical-microcanonical averages are compared to their corresponding canonical ensemble averages, obtained through standard Monte Carlo computations. A major disagreement is found, because the canonical ensemble seems to have completely lost any information about the phase transition. The microcanonical ensemble appears as the only reliable statistical framework to tackle self-gravitating systems. Finally, our results -- obtained in a ``microscopic framework -- are compared with some existing theoretical predictions -- obtained in a ``macroscopic (thermodynamic) framework: qualitative and quantitative agreement is found, with an interesting exception.
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