The object of study is the vertical wave propagation in a sand deposit. This paper is aimed at analyzing the vertical wave propagation in a sand deposit through micromechanical modeling that inherently takes account of intergranular slips during deformation. Such a problem, which is part of the general framework of wave propagation in the soil, has long been analyzed using continuum models based on approximate behavior laws. For this purpose, a 2D Discrete Element Method (DEM) model is developed. The DEM model is based on molecular dynamics with the use of circular shaped elements. The intergranular normal forces at contacts are calculated through a linear viscoelastic law while the tangential forces are calculated through a perfectly plastic viscoelastic model. A model of rolling friction is incorporated in order to account for the damping of the grains rolling motion. Different boundary conditions of the profile have been implemented; a bedrock at the base, a free surface at the top and periodic boundaries in the horizontal direction. The sand deposit is subjected to a harmonic excitation at the base. Using this model, the fundamental and resonance frequencies of the deposit are first determined. The former is determined from the low-amplitude free vibration and the latter by performing a variable-frequency excitation test. It is noted that there is a significant gap between the two frequencies, this gap could be attributed to the degradation of the soil shear modulus in the vicinity of the resonance. Such degradation is well proven in classical soil dynamics. The effects of deposit height and confinement on resonance frequency and free-surface dynamic amplification factor are then investigated. The obtained results highlighted that the resonance frequency is inversely proportional to the deposit’s thickness whereas the dynamic amplification factor Rd increases with the deposit’s thickness. In the other hand, when the confinement increases the deposit becomes stiffer, which results in reducing the amplification. Such result is in accordance with theoretical knowledge which states that the most rigid profiles such as rocks do not amplify seismic movement.