Figure 3. Potential of Mean force for conduction events with two Na⁺ ions.

Values on the x/y-axis correspond to distances along the pore axis between the permeating ions and the centre of the carbonyl oxygen atoms of residues Thr175 (d1) and Leu176 (d2) respectively. Counter lines are drawn every 1 kcal/mol. Snapshots from the umbrella sampling trajectories are shown for some significant configurations. Residues 175 to 178 of two opposite subunits are depicted in licorice representation, together with the permeating Na⁺ ion (yellow). Water molecules closer than 5 Å (licorice representation) and 15 Å (grey lines) to the ion are shown. The minimum energy path between a minimum with one ion in the cavity and a minimum with one ion in extracellular solution is shown as a black line. The free energy along the minimum energy path is shown in Figure S3.