In the present work, molecular dynamics is used to study molecular nitrogen impinging on multilayered graphene and fused-quartz surfaces at different incidence speeds and angles to obtain energy accommodation coefficients for use in direct-simulation Monte Carlo. The trajectory molecular dynamics simulations were performed on these two surfaces to study the difference between atomistically smooth and rough cases. Based on the postcollision behavior of the nitrogen molecule, the molecular dynamics trajectories were classified into three categories, namely, single, and multiple with and without escape. The collision statistics for the three categories were found to depend on the incidence angle and the speed, and a strong correlation among incidence speed, angle, and surface topology in the probability distribution of the energy accommodation coefficients was observed. A direct-velocity-sampling gas–surface interaction model was implemented in direct-simulation Monte Carlo, which was found to predict flow and surface properties comparable to the Maxwell gas–surface interaction model when the molecular dynamics data used for velocity sampling were obtained from a rough (diffuse) surface.