In this talk I will introduce a method to measure the phonon dispersion of a crystal based on molecular dynamics simulation which has been implemented as an extension to an open source classical molecular dynamics simulation code LAMMPS. In the proposed method, the dynamical matrix is constructed by observing the displacements of atoms during molecular dynamics simulation, making use of the fluctuation-dissipation theory. The dynamical matrix can then be employed to compute the phonon spectra by evaluating its eigenvalues. It is found that the proposed method is capable of yielding the phonon dispersion accurately, while taking into account the anharmonic effect on phonons simultaneously and therefore providing a superior alternative to existing methods. Other ongoing projects on computational materials science in my group will also be mentioned.