What length scale properties are you interested in? Not all MD code deals with momentum the way you might want. Are you interested in molecular diffusion, surface energy, or something else? If you want to deal with interacting particles in flow then maybe you may want to consider lattice-boltzmann simulations.

Example article:

Article Hydraulic fracture conductivity: effects of rod-shaped propp...

Code:

http://optilb.org/openlb/

Dear Matthew

Thanks for your suggestions. I wanna using MDs to simulate the effect of coating nano particles on the placement of proppant at nano fractures (at the tip of fracture), is that possible?

Regards

LAMMPS is a good MD code for materials research.