The statistical thermodynamics of a classical system composed of rigid molecules is considered in the molecular dynamics ensemble. Accepting Boltzmann’s S=k(B) In W as the basic assumption of statistical mechanics, exact formalisms for two classical choices of W are derived. Since there are no restrictions on the order of thermodynamic derivatives, any measurable quantity is directly accessible in this ensemble. Explicit statistical analogs are given for the derivatives of the Helmholtz energy including an approximation for the chemical potential, Basic phase space functions are identified and their properties are explored. It is shown that the complete thermodynamics is governed by small perturbations of these functions from universal behavior.