In this study modeling different structures in perturbed Poiseuille flow in a nanochannel by using of molecular dynamics simulation was performed. Nanochannel limited by parallel Platinum plates containing an Argon fluid. We found that the wall roughness increases the velocity in the nanochannel by shrinking the cross-section. Also, the rectangular roughness and hemispherical roughness have the maximum and minimum effects on the flow properties, respectively. The other result is that the nanochannel roughness reduces the range of fluctuations near the walls. This is due to the fact that less fluid particles reside in the vicinity of the rough nanochannel walls compared the ideal nanochannel. Finally, changing the configuration of the nanochannel roughness from ellipsoid to hemi-spherical increases the number of Pt atoms in the structure and the simulated system; therefore, the total energy is also expected to increase. •Modeling different structures in perturbed Poiseuille flow.•Study the equilibrium.•Using of molecular dynamics simulation.