Atomic simulation methods modelling fluid flows often incorporate in the equations of motion the steady state flow profile predicted by Navier-Stokes equations. We show in this work that this may lead to significant errors such as spurious shear induced ordering, unphysical steady state flow profiles or artificial dampening of thermal motion even at shear rates regarded as low in simulation applications. Our results also suggest that nonequilibrium molecular dynamics coupled with the recently developed configurational thermostat, which makes no assumption at all on the flow profile, provides a much more realistic way to study these phenomena. (C) 2003 American Institute of Physics.