Currently there are two Poisson solvers implemented in BioMOCA based on the finite difference method. One uses the pre-conditioned Conjugate Gradient scheme (pCG) and is used by default. The later is borrowed from an APBS solver, which uses a V-multi-grid scheme. Other than the numerical approach to solve the Poisson equation, the main difference between the two solvers is on how they address the permittivity in the system. In the first solver, a dielectric value is assigned to each cell in the grid, while in the APBS solver the dielectric coefficients are defined on the grid nodes. As discussed earlier box integration method is used in the pCG solver, which treats the Poisson equation in the most accurate way. Even though a full multigrid solver based on box-integration method has been under development, there is a neat way to reuse the already exiting code and treat the ion channel systems.