A Molecular Dynamics computer simulation model for describing proton transport in biomolecular systems will be reviewed. The development of the underlying computational method which allows us to study the structural and dynamical properties of excess protons in these channels will first be discussed. Several applications of the methodology to study proton transport in channel environments will then be described. In each case, insight will be provided into the atomistic factors which determine the proton transport rate and the underlying mechanism(s) for the proton hopping process. More extensive background and results for the M2 channel in the influenza A virus will also be presented.