  In molecular dynamics simulations, nanochannel flows are usually driven by a
constant force, that aims to represent a pressure difference between inlet and
outlet, and periodic boundary conditions are applied in the streamwise
direction resulting in an homogeneous flow. The homogeneity hypothesis can be
eliminated adding reservoirs at the inlet and outlet of the channel which
permits to predict streamwise variation of flow properties. It also opens the
door to drive the flow by applying pressure gradient instead of a constant
force. We analyze the impact of these modeling modifications in the prediction
of the flow properties and we show when they make a difference with respect to
the standard approach. It turns out that both assumptions are irrelevant when
low pressure differences are considered, but important differences are observed
at high pressure differences. They include the density and velocity variation
along the channel (the mass flow rate is constant) but, more importantly, the
temperature increase and slip length decrease. Because viscous heating is
important at high shear rates, these modeling issues are also linked to the use
of thermostating procedures. Specifically, selecting the region where the
thermostat is applied has a critical influence on the results. Whereas in the
traditional homogeneous model the choices are limited to the fluid and/or the
wall, in the inhomogeneous cases the reservoirs are also available, which
permits to leave the region of interest, the channel, unperturbed.
