For molecules that adopt folded conformations in AA-MD simulations, execution mode 2 typically provides increased flexibility in the optimized CG models, which allows to reproduce the dynamical properties of the molecules as an "effect" rather than a pre-encoded condition in the models. This is particularly important when one may want to develop models for molecules composed of rather flexible groups, which then are supposed to interact between them or with other molecules in the simulations. In fact, this may limit spurious effects arising from too rigidly parametrized BP (eventually coming from the reduced timescales accessible by common AA-MD simulations) that may then affect how molecules interact between them. Although less automatic, mode 2 has the advantage of not using the software as a black box, but at the same time it requires a prior knowledge of the molecular system that is not always accessible. In such a case, the user can always use Swarm-CG in mode 1, which in principle should provide the best accessible bonded parametrization. We included the option to select either usage mode to leave maximum freedom to the user, with standard or more advanced usage of the software.