Advanced Energy Systems and Microfluidics Laboratory

Introduction to Computational Physics by Franz Vesely

This is a very good place to start with the prerequisites of Molecular dynamics.

Related Links

A notable paper on Molecular Dynamics

This was one of the important papers published on Molecular Dynamics.

Michigan Tech—Mechanical Engineering

The MTU Mechanical Engineering home page.

Loren on the Art of MATLAB

A very interesting and informative blog on MATLAB and its arcane working!