The collective variables nomenclature follows the same formulation originally developed by Hub and collaborators and our previous works in membrane fusion and fusion pore nucleation. Conceptually, ξ f and ξ n are analogous (see eqs. 1 and 2). Each one defines a cylinder of radius R cyl with N s slices of thickness d s that can be filled by any user-defined Vesicle connected with the plasma membrane through a fusion pore. c) Spanning cylinder that defines collective variable ξ f to fuse hemilayers (gray). d) Cylinder connecting the intra-organelle space with the extra-cellular milieu that defines ξ n and nucleates the fusion pore (green). e) Expansion of the fusion pore with collective variable ξ e using the single-slice cylinder (orange).