Using lattice dynamics theory, we derive the spectral energy density and the relation between the spectral energy density and the phonon frequencies and relaxation times. We then calculate the spectral energy density and phonon frequencies and relaxation times for a test system of Lennard-Jones argon using velocities obtained from molecular dynamics simulations. The phonon properties, which can be used to calculate thermal conductivity, are compared to predictions made using (i) anharmonic lattice dynamics calculations and (ii) a technique that performs normal mode analysis on the positions and velocities obtained from molecular dynamics simulations.