We have conducted all our simulations with the MARTINI coarsegrained model 26 using SMACs parameters developed by Orekhov et al. . In all cases the bilayers used were POPC:POPS:POP2 in concentrations (85:10:5), constructed with the CHARMM-GUI web server . All bilayers contained 1024 molecules each (≈17x17nm), which ensures negligible finite-size effects due to interactions between periodic images of the fusion pore . Each bilayer was initially solvated in more than ≈15x10 3 PW coarsegrained polarizable water molecules to fulfil the ample water condition for MARTINI . When merged together, the amount of extra-organelle water molecules (confined between the bilayers) was adjusted to equilibrate the inter-membrane separation distance at ≈3.5nm, in resemblance to the protein-mediated fu-sion pore stabilization by one synaptotagmin-1 C2B domain . It has been suggested that inter-membrane distance could also be a mechanism to stabilize fusion pores against re-closure 41 . For a detailed description of inter-membrane distances effects, see Smirnova et al. . Molecular dynamics simulations were performed with GROMACS-2020.2 with the semi-isotropic NPT ensemble and a time step of 20fs in all cases, with the exception of the simulation of a single SMAC solvated in water (no bilayers) where the isotropic ensemble was used instead. The temperature, T=303.15K , was controlled by a V-rescale thermostat using a coupling constant of 1ps. The pressure was maintained at 1.0bar and compressibility was set to 3x10 -4 bar -1 . For equilibration runs the Berendsen barostat was used with a time constant of 5ps while for production the Parrinello-Rahman barostat was used instead, with a time constant of 12ps. Neighbour searching was performed using a Verlet cut-off scheme with a buffer tolerance of 0.005kJ/mol/ps. The minimum frequency to update the neighbour list was set to 20 steps with periodic boundary conditions (PBC) in all directions. The reaction field method was employed for Coulomb interactions with a cut-off of 1.1nm and a relative dielectric constant of 2.5. Van der Waals interactions were treated using the cut-off scheme with a cut-off of 1.1nm. Before production runs, all systems were minimized and equilibrated for at least 100ns to generate properly relaxed initial configurations.