Practically, D and R 0 are defined as input parameters for collective variable ξ e at the beginning of simulations. From the value of ξ e extracted from molecular dynamics trajectories, eq. 8 gives R eq , which introduced in eq. 7, gives the radius at the neck of the toroid-shaped water channel R ef f . Therefore, R ef f becomes a convenient measure of the fusion pore dilation. Although almost linear with it (see figure ), ξ e is a dimensionless parameter with less intuitive physical meaning.