AA data used to set the target of the optimization procedure include a structure and trajectory files. The AA structure with atom types, connectivity, masses and charges can be provided via a GROMACS portable topology file (.tpr). The AA trajectory can be provided in any GROMACS format accepted by MDAnalysis (.xtc, .trr or else). Periodic boundary conditions (PBC) are handled internally if the trajectory file includes position and size of the simulation box at each time step. Otherwise, it is assumed PBC have already been handled and a warning is displayed at start of the program. The AA trajectory is mapped on-the-fly to allow faster experimentation with different mapping schemes. The mapping of atoms to CG beads must be provided as a GROMACS index file (.ndx). The weight of atoms that would be mapped to multiple CG beads will be split accordingly when performing the mapping and calculating all AA-mapped reference geoms distributions. The preliminary CG model to be optimized must be provided as a GROMACS topology file (.itp), along with the non-bonded interactions force field to be applied in MD simulations. To better handle sampling in symmetrical molecules, users can easily form groups of bonds, angles and dihedrals in this topology file (using line returns or comments). AA-mapped distributions will be averaged within groups to create the references used as target of the optimization procedure, and shared parameters will be used and optimized for the geoms of each group. This also makes the optimization process more efficient by reducing the number of free parameters. For example, grouping 5 angles together reduces the number of associated free parameters from 10 to 2 when using execution mode 1 and GROMACS angles functions 2. Swarm-CG requires users to provide a GROMACS structure file (.gro) to be used as the starting conformation of each simulation step during the iterative optimization process. This structure will be (i) minimized and (ii) pre-processed before gathering data from the production run (iii), using three userprovided GROMACS MD parameters files (.mdp), one for each step. Only the simulation parameters of the production run will be modified to adapt its number of steps and the number of frames of the output trajectory to be analyzed, according to software parameters (1000 frames by default, within 10 or 25 ns). Although the starting conformation does not have to be perfectly accurate, as it will be minimized and pre-processed at start of each iteration, this conformation must allow running stable simulations while exploring different sets of bonded parameters. For example, molecular modelers can make use of an initial set of MARTINI bond parameters just stable enough to obtain a preliminary CG model file and a starting conformation to be used for the optimization phase. The following GROMACS bonded potential functions are implemented, which should be necessary and sufficient for building CG models: constraints function 1, bonds function 1, angles functions 1 and 2, and dihedrals functions 1, 2, 4 and 9. Swarm-CG can effectively optimize parameters for dihedrals potential functions with multiplicity greater than one, although these may be used carefully as they are known to easily trigger instabilities in simulations. During optimization, sets of BP (i.e. particles of the swarm) that cause simulations to terminate abruptly gets attributed the worst possible score the scoring function can yield, according to given topology and geoms domains.