No (d) Yes Yes ± 25% x EMDbest/n (c) ± 30% x EMDbest/n (c) 3 Yes Yes Yes ± 15% x EMDbest/n (c) ± 20% x EMDbest/n (c) (a) Dihedrals parameters are optimized only in cycles 2 and 3, if dihedrals topologies are provided in the input preliminary CG model. Applied to values of 0.025 nm for bonds or 10° for angles and dihedrals, to define the lower/higher range of variations around previous equilibrium values during swarm initialization (for optimization cycle 1, those are obtained via BI). EMDbest is the EMD score obtained for a given geom in the previously obtained best scored model, while n=2 for bond and angle groups and n=5 for dihedral groups. In cycle 2, bonds parameters are fixed to those of the previously obtained best scored model. Additionally, one special particle is initialized at start of optimization cycles 2 and 3. Across optimization steps, each time the EMD score of an independent geoms group distribution improves, its associated subset of parameters is recorded (i.e. equilibrium value and force constant of the geoms group). For swarm initialization the next optimization cycle, these are combined into a single special particle. This heuristic, which works like a "memory of independent best", is expected to accelerate convergence of the iterative optimization procedure by providing either a new best solution, or useful information to the rest of the swarm.