In this study, we have used multiple GPUs to simulate three dimensional ion flow through a pentameric ion channel extracted from COVID-19 E protein. The problem is formulated using Poisson-Nernst-Planck (PNP) equations in conjunction with Lennrad Jones potential. We are using Immersed Boundary-Lattice Boltzmann Method (IB-LBM) to solve the system of equations. Further we have compared the performance of different sets of GPUs and implemented further parallelization to take full advantage of concurrency and data structuring.