To simulate the structure and dynamics of biomolecules, we approximate them as
*a physical network of balls that have point charges at their centers and are connected
by springs*. In addition to springs that govern the bending of bonds and angles, there are forces
that favor certain rotations about the bonds. The balls representing the atoms are not hard spheres;
they are Lennard-Jones particles that can overlap each other. Our goal is to study the motion of
this physical network of balls and springs, in hopes of interpreting and predicting the dynamics of
real macromolecules at the atomic level.

- A Note on Notation - Some CHARMMing language
- Simulating Biomolecules: The Three Necessary Ingredients

Peter J. Steinbach 2010-11-15