In order to apply the molecular dynamics (MD) method to simulate modulated phases in organic materials, a compensating external pressure tensor is proposed to compensate for the deficiencies of the force field applied in the simulation. MD can well reproduce modulated phases that have been measured by diffraction. Mechanisms of incommensurate modulation are revealed from the simulations. Details of the structures relating to the origins and mechanisms giving rise to the formation of modulated phases are presented.