We performed the same study for the NDI-based molecules, the results of which are reported in Figure and compared to the CG model available from the literature. Using execution modes 1 and 2, the initial BIs yielded inappropriate sets of BP, notably due to the several dihedral potentials used to maintain the planarity of the molecular core (Figures ). During optimization with mode 1, BP scores decreased from 182.2 to 41.3 and allowed to retrieve a correct planar geometry of the core of NDI, with correctly adjusted geoms distributions (Figure ). Average Rg value of the optimized model is in perfect agreement with the AA-mapped reference trajectory (Figure : ΔRg = 0.5 Å or 4.8%). BP optimization converged within 395 steps (Table ). As a comparison, the manually parametrized CG model of NDI yielded a higher BP score of 74.42 in a 200 ns simulation, indicating some geoms distributions could be better adjusted (Figure ), although average Rg was correct at 11.7 Å (ΔRg = 0.7 Å or 6.8%). Using execution mode 2, BP scores went down from 350.2 to 52.4 and produced geoms distributions almost indistinguishable from those obtained using mode 1, since only the hinge junctions between core and arms (Figures S17, angle groups 10 and 11) used angles at 180° and those where already "loosely" adjusted with mode 1 (although Swarm-CG selected an equilibrium value at 120°). In both resulting models, the low force constant associated to the hinge junctions should not restrict the full extension of the arms, and thus is not expected to significantly affect assembly simulations, but these specific flexibilities must be considered carefully. Average Rg was 11.8 Å (ΔRg = 0.8 Å or 7.8%). BP optimization converged within 301 steps.