Simulation of fluid properties and flow below a certain length scale, where the continuum assumption does not hold any more, has to be done on a molecular level. Molecular Dynamics (MD) is a proper tool for nanofluidics. The limits of the system sizes manageable today are pushed not only by advances and availability of new hardware. It's even more important to achieve enhancements in the development of fast efficient algorithms and hardware optimized implementations. High Performance Computing systems and especially Clusters of Workstations, which turn out to be very well suited for this task, are the primary target platform for the majority of MD codes today. After a classification of the flow type addressed here, implementation details and parallelization strategies will be discussed for MD simulations based on short-range potentials, suitable for a rich variety of components.