Voltage-gated calcium channels are the primary mediators of depolarization-induced calcium entry into neurons [1]. While calcium channels are of critical importance to brain function, their inappropriate expression or dysfunction gives rise to a variety of neurological disorders, including, pain, epilepsy, migraine, and ataxia. Molecular dynamics methods are the only physically valid methods for studying the structure function relations in ion channels. Applications of these methods to sodium and calcium channels are presented, which illustrate the multi-ion nature of the permeation mechanism in selective biological channels (as shown in Figure 1). In this study, we present binding energies of single and multi-ion Na+ to the Ca++ channels. Furthermore we interpret binding energies for constructing structure-function relationship of this channel