Time series of the RMSD of PTx2 backbone atoms relative to the VSD compared with the initial structures. (A–D) RMSD plots from (A) deactivated VSD II, (B) activated VSD II, either isolated or attached to the channel, (C) deactivated VSD IV, and (D) activated VSD IV, either isolated or attached to the channel, are displayed for three MD simulation replicas each. The colored bold lines represent the moving averages calculated over intervals of 10 ns each, while the gray lines represent the raw values. The MD simulation equilibration period is shown as a light green box.