In full-atomic molecular dynamics simulations of ion channels, most of the computational cost is for following the trajectory of water molecules in the system. However, in BioMOCA the water is treated as a continuum dielectric background media. In addition to that, the protein atoms of the ion channel are also modeled as static point charges embedded in a finite volume with a given dielectric coefficient. So is the lipid membrane, which is treated as a static dielectric region inaccessible to ions. In fact the only non-static particles in the system are ions. Their motion is assumed classical, interacting with other ions through electrostatic interactions and pairwise Lennard-Jones potential. They also interact with the water background media, which is modeled using a scattering mechanism.