The expanded bonded parameter set was first fitted in two stages. First against a diverse set of atomistic reference simulations using the CHARMM36 force field (see simulation details in Methods Section 3.1). The atomistic reference simulations were all mapped to pseudo-CG trajectories (Figure ,B-C) using our newly proposed mapping scheme (Figure ,A) and equivalent CG simulations were prepared for each system. Then the CG bonded distributions were fitted to the mapped atomistic counterparts in a bottom-up approach, employing manual adjustments and automatic protocols like swarm optimization .