The objective of this project is to develop computational tools, based on molecular dynamics methods, to simulate the flow in ducts to transport CO2, CH4 and oil. The main goal is to have a better understanding of the interaction of the wall material and the fluid. Our intention is to use such tools to investigate, for example, hydrophobic polymers optimized to mitigate the head loss and, consequently, the energy required to transport CO2, CH 4, oil and multiphase fluids in ducts. With the molecular dynamics methodology, the interaction between the fluid and the duct coating material is properly evaluated. The no slip boundary condition is not considered a priori. Instead, the shear stress exerted by the fluid in the wall is used as a boundary condition for the simulation employing a numerical technique which considers the fluid as a continuum media. We first solve the flow at the molecular level in the vicinity of the wall. The shear stress is obtained and this is employed as the boundary condition for the solution of the Navier-Stokes equations for the remainder of the domain.