Sure! Checkout LAMMPS (http://lammps.sandia.gov/) and these tutorials https://icme.hpc.msstate.edu/mediawiki/index.php/LAMMPS_tuto...

Also, check out Molecular Dynamics Simulation (http://www.amazon.com/Molecular-Dynamics-Simulation-Elementa...)

and Computer Simulation of Liquids (http://www.amazon.com/Computer-Simulation-Liquids-M-Allen/dp...)