Our new simulation scheme in isosurface-isothermal-isobaric ensemble [Eslami, H.; Mozaffari, F.; Moghadasi, J.; Muller-Plathe, F. J. Chem. Phys. 2008, 129 194702], developed to simulate confined fluids in equilibrium with bulk, is applied to simulate polyamide-6,6 oligomers confined between graphite surfaces. The reverse nonequilibrium molecular dynamics simulation technique is employed to shear the graphite Surfaces. In this work, six confined systems, with different surface separations, as well as the bulk fluid are Simulated. Our results show a viscosity increase with respect to the bulk fluid, with decreasing distance between surfaces. Also, the calculated viscosities of the confined systems show an oscillatory behavior with maxima corresponding to well-formed layers between the surfaces. We observe a Substantial slip at the surfaces, with the slip length depending on the shear rate and oil the slit width. The slip length and the slip velocity show oscillatory behavior with out-of-phase oscillations with respect to the solvation force oscillations. Moreover, the temperature difference between coldest and hottest parts of the simulation. box depends oil the shear rate and on the layering effect (solvation force oscillations). An analysis of oligomer deformation Under flow shows preferential alignment of oligomers parallel to the surfaces with increasing shear rate.