The more recent GōMartini 3 model, implemented on the Martini 3 framework (98), represents a significant advancement over its predecessor, GōMartini 2. This new methodology addresses several limitations of the earlier version. Unlike GōMartini 2, which defined interacting residue pairs directly in the protein topology file, GōMartini 3 introduces virtual interaction sites placed on the BB beads (near the C𝛼 atoms). These virtual sites define the interactions between residue pairs using LJ potentials, enabling better computational efficiency through parallelization and the implementation of non-bonded cutoffs. Although the contact map remains the same, GōMartini 3 defines contacts based on a specified BB-BB distance, ranging from 0.3 to 1.1 nm. This refined distance range helps to eliminate artifacts caused by high bead density or by interactions between residues that are too distant to influence the protein's structure and flexibility . Additionally, to prevent structural distortions, non-bonded interactions between BB beads are excluded for residue pairs defined by virtual interaction sites. This exclusion improves the packing of protein structures and enhances their stability during simulations.