The molecular dynamics (MD) computer simulation method is a well established and important tool for the study of the dynamical properties of liquids, solids, and other systems of interest in Materials Science and Engineering, Chemistry and Biology.

A material is represented in terms of atoms and molecules. The method of MD simulation involves the evaluation of the force acting on each atom due to all other atoms in the system and the numerical integration of the Newtonian equations of motion. Though MD was initially developed to compute the equilibrium thermodynamic behavior of materials (equation of state), most recent applications have used MD to study non-equilibrium processes.

Wikipeda offers a basic introduction to molecular dynamics with many references:

http://en.wikipedia.org/wiki/Molecular_dynamics

For a thorough treatment of MD methods, see:

"Computer simulation of liquids" by M.P. Allen and D.J. Tildesley (Oxford, 1989) ISBN-10: 0198556454 | ISBN-13: 978-0198556459.

For an understanding of MD simulations and application to statistical mechanics:

"Understanding Molecular Simulation, Second Edition: From Algorithms to Applications," by D. Frenkel and B. Smit (Academic Press, 2001) ISBN-10: 0122673514 | ISBN-13: 978-0122673511
"Statistical and Thermal Physics: With Computer Applications," by H. Gould and J. Tobochnik (Princeton, 2010) ISBN-10: 0691137447 | ISBN-13: 978-0691137445

CoMD implements both the Lennard-Jones Potential (ljForce.c) and the Embedded Atom Method Potential (eam.c).