The recent solution of X-ray structures for the bacterial channel NavAb has provided the first opportunity to study functional mechanisms of voltage-gated sodium channels at the atomic level. NavAb is reminiscent of voltage gated K+ channels but present a wider selectivity filter, lined by the side chains of 4 glutamates, usually indicative of a calcium-selective mammalian channel. Despite this contradiction, nominal selectivity of Na+ over Ca2+ is observed experimentally, and has been proposed to arise from the ability of the channel to accommodate and efficiently conduct a specific number of charges, while the difference between Na+ and K+ is generally attributed to the stronger affinity of carboxylate oxygens for smaller ions (high field strength). We carry out multi-μs fully-atomistic simulations, using the purpose-built Anton supercomputer, to extract representative conformations for all occupancy states of the pore and carry out Free Energy Perturbation calculations to determine the relative free energies of Na+, K+ and Ca2+ throughout the selectivity filter. We then explore the movements of multiple ions on the multi-μs timescale to construct unbiased free energy landscapes for conduction for each of the 3 ionic species. Our simulations provide new understanding of the fundamental interactions governing selective ion conduction in sodium channels1 .