List of Figures

1. Graph of van der Waals potential with and without switching
2. Graph of electrostatic potential with and without shifting function
3. Graph of electrostatic split between short and long range forces
4. Example of cutoff and pairlist distance uses
5. Dual topology description for an alchemical simulation. Case example of the mutation of alanine into glycine. The lighter color denotes the non-interacting, alternate state.