Ion channels are highly charged proteins that reside in the membrane of all living cells to regulate charge transport to the cell. Most channels have device-like behaviors that are interesting to the electronics community for their possible application in bio-device design. Simulating ion channels over time-scales relevant to conduction present a difficult time and space multi-scale problem that is beyond the scope of the Molecular Dynamics approach. To address this problem we have developed BioMOCA, a 3-D reduced particle ion channel simulator based on the transport Monte Carlo methodology. BioMOCA has been described elsewhere; here we use it to study the link between the electrostatic properties of the protein and selectivity in the gramicidin channel. We also present representative simulations of Na+ transport in gramicidin.