The aim of this study is refinement of proton(s) hopping rate by applying new model for Molecular Dynamics (MD) calculation with Empirical Valence Bond (EVB) method. The overview about this new model is an acceptor selection method based on energy prediction instead of the one based on distance. The effect of water molecules outside the Eigen cation was mainly considered in this new model. Then, microenvironment interaction to the formation of the cluster and proton hopping were reasonably expressed as an actual condition. This procedure was applied for proton hopping. The total number of cluster formation and cancel were also analyzed.