Nonequilibrium molecular dynamics simulation is applied to investigate the effect of periodic wall roughness on the flow of liquid argon through krypton nanochannels. The effect of the length of a rectangular protrusion on the flow is investigated and compared to the case of nanochannels with flat walls. The results show a clear trapping of fluid atoms inside the rectangular cavities that are formed between successive protrusions. The size of the cavities affects the potential energy map and, consequently, fluid atom localization. This localization results in a reduction of velocity values inside the cavities, as well as a reduction of the slip length near the rough wall.