All-atom membrane systems for different lipids were set up using CHARMM-GUI, 44 number of lipid molecules was ∼80, depending on the system. After equilibration, all atomistic MD simulations were run for 100 ns, using a time step of 2 fs, with the CHARMM-36m force field in GROMACS 2021.5. Temperature control above the melting temperature T m of each lipid was ensured by using the CSVR thermostat, with τ T = 1 ps, and the pressure was maintained at 1 bar using the semi-isotropic cell rescale barostat, with τ P = 5 ps. PME was used to compute long-range electrostatics, with a real space cut-off radius of 1.2 nm. The same cut-off was also used for the Lennard-Jones interactions, and bonds involving hydrogen atoms were constrained with LINCS. The all-atom trajectories were then coarse-grained using the PyCGTOOL package and the MARTINI 2 mapping. The mapping and bead types used for the parametrization are shown in Fig. , where beads represented by the same color in different lipids have the same χ parameters. The bond distances were calculated from the average distances in the atomistic trajectories (see Table in the Supporting Information), while the reference angles for the three-body interatomic potential and all harmonic force constants were taken from MARTINI. We computed the reference lateral density profiles with MDAnalysis from these CG-mapped trajectories, and used them in the differentiable MD optimization.