Swarm-CG is designed for usage with the GROMACS MD engine. In this paper we demonstrate Swarm-CG performances to optimize CG models built based on the well-known MARTINI force field. However, the workflow of Swarm-CG is general and it can be used for refining basically any CG model, provided that non-bonded parameters and a mapping scheme are defined, and a reliable reference trajectory is available. The necessary input can be divided in two groups: (i) AA data used to define the target of the optimization and (ii) preliminary CG data used to perform the model optimization. The AA input data (i) include a well-sampled MD trajectory of the AA molecular model to be used as reference and its pre-defined mapping to CG beads. We note that while a few automatic AA-to-CG mapping schemes have been already proposed (e.g. in the MARTINI formalism), these typically work only for small molecules. The search of methods suggesting the best CG representation for accurately treating the dynamics and structural features of molecules is a subject of great scientific debate. Here, for sake of a broader practical utility of Swarm-CG, we preferred to leave the AA-to-CG mapping to the user, who is free to choose the preferred CG scheme (the MARTINI force field or other pre-set schemes), while the software will optimize the bonded terms accordingly. Input CG data (ii) include a preliminary CG model, together with its non-bonded force field parameters, and simulation setup for the iterative MD simulations that will be used for the model refinement: i.e. the starting molecular configuration and the MD parameter files (cf. section 6.1). The starting molecular configuration will be minimized and pre-processed at each iterative MD simulation step using new sets of BP. The preliminary CG model needs to contain relevant information on the CG beads (e.g. type, charge, mass), the bonded potential topology and functional forms (which define the form of Eq. 1), while equilibrium values and force constants are arbitrarily initialized (e.g. to 0). Symmetries of the CG topology can be specified in the preliminary model file to improve the quality of the reference AA sampling and to reduce the number of free parameters to optimize. To this end, the bonds (or angles, dihedrals) that are structurally equivalent due to molecular symmetries can be gathered in "groups" so that: (i) their distributions are averaged in the analysis and (ii) they share the same BP (cf. section 6.1). Groups of geoms are directly indicated by the user in the preliminary model file. Swarm-CG provides detailed documentation and uses a set of default filenames for easier arguments handling.