A molecular system containing each unique disaccharide is then set up (automatically) in a box of water and subjected to energy minimization, equilibration and production MD simulations as per the protocols described in the Methods. The code then extracts the equilibrium bond lengths, angles and dihedrals as well as their associated force constants from the resulting atomistic data using our previously reported PyCGTool package . Concurrently an all-atom to CG mapping protocol is applied (Figure ), which is based on the standard Martini 3 rules and in line with the mapping optimized for monosaccharides . A coarse-grained bead will typically be mapped from the center of geometry of 4 heavy atoms and their bonded hydrogens of a functional group. Figure shows the mapping scheme followed in this work for chemical moieties present in the hexoses. This mapping strategy derives from previously published Martini 3 carbohydrate parameterization work with their associated bead type used to model the chemical properties in Martini 3. A particularity of the new Martini 3 model is the use of a virtual site in the middle of the ring moiety (purple sphere in Figure ). Adding a virtual site (massless hydrophobic bead) has been shown to help model interactions between cyclic groups (ring stacking). In this version of the disaccharide coarse-graining strategy, we have avoided the 15% expansion in bonds forming part of the ring (which has previously been reported ) in order to (i) make the comparison to all-atom models more straight-forward and (ii) simplify the pipeline.