One of the most important equations in fluid mechanics is the Navier-Stokes equations which has no exact solution which is due to its great complication and a number of parameters which are involved. Besides, most of the equations which are applied in ordinary scales will fail in small scales or will not have sufficient accuracy. Fluid slip is one of the important phenomenon in fluid flow in ducts and channels which is neglected in ordinary scales (meter or millimeter), and no slip boundary condition is applied to solve fluid equations. Surface phenomena's such as flow slip is dominant in micro and nano scales. This is due to the fact that the ratio of surface to volume in such scales is relatively high. Fluid slip should be investigated in small scales especially in nano-devices to truly analyze the behavior of fluid flow. In the present work it is intended to study the effect of various parameters which are dominant in fluid slip such as the effect of channel height, interaction between solid and fluid particles, surface roughness, roughness periodicity, wall velocity, and atomic size. It should be noted that the LAMMPS program have used for the simulations which is one of the efficient and powerful available software's which is used for fluid flow simulations usually in nano-scales. According to the simulation results, fluid slip will decrease as the channel height increases in Couette flow with constant wall velocity. Also the relation between slip length and the channel height has a power law behavior. By increasing the velocity of moving wall, slippage will be greater, and velocity profiles will have nonlinear behavior in both flat and rough channels. However, some parts of fluid particles are almost stationary and have no sensible velocities in higher wall velocities. Increasing the interaction between the fluid and wall particles will result to have great effects on the velocity profiles in a flat channel, and slip velocity will decrease. In all cases, velocity of fluid particles near rough walls is close to the wall velocity and slip length in the channels with both rough walls will increase almost linearly. Slip length will extremely decrease with increasing the roughness height or decreasing the distances between corrugations and fluid flow will be blocked by the effect of roughness. In these cases both slip velocity and slip length are negative according to the locking boundary which originates from the blocking effect of the fluid particles by corrugations. Different shapes of roughness such as rectangular, triangular, right and left triangles have been used. Rectangular roughness generates the most resistance against the fluid flow and makes the fluid particles stationary. So it has been noticed that the slip length and slip velocity near the rough walls have negative magnitude in almost all simulation cases. Right and left triangular shapes have nearly the same behavior on the velocity profiles and almost the same magnitude of slip length is detected. Increasing the distances between corrugations which is equal to increase the channel periodicity will make the velocity profile to have the behavior like flat channel and increase the slip velocity. Keywords : Molecular dynamics simulation, nano-channel, slippage, slip length, rough channel