The application of ξ e to the fusion pore completes the free energy landscape together with ξ f 19,28 and ξ n . As demonstrated before, these collective variables show negligible hysteresis and allow for effective free energy calculations using restrained molecular dynamics simulations. Figure shows schematically the full profile along the life of the fusion pore, from initially flat and parallel bilayers until expansion. The fusion stalk region (lilac) corresponds to our previous study on membrane fusion 28 using collective variable ξ f . Fusion pore nucleation (pink) was also described previously. A gap in the transition from nucleation to expansion still exists and is indicated in the PMF by a dashed line in the pink region. Fusion pore expansion is colored green and is described in this study using collective variable ξ e . Expansion beyond R ef f ∼ 0.8nm (marked by the dashed line in the gray region) can be directly obtained using collective variable ξ e , however, larger R ef f may require larger membrane patches to avoid finite size effects.