A combination of coarse-grained (CG) and atomistic simulations provide a suitable com-putational framework to study unstructured regions of proteins, for which experimental data is often lacking or limited. In this work, we combine CG and atomistic simulations with cluster-ing algorithms and free energy reweighting methods to explore the conformational equilibrium of certain regions of the salt-stable cowpea chlorotic mottle virus (SS-CCMV). In particular, we focus on the geometry of converging strands (residues 26–49) from contacting subunits at the 3-fold (hexamer) and 5-fold (pentamer) symmetry points of the capsid. We show that (i) the simulations reproduce the experimentally observed β barrel for the hexamer; (ii) the 1 pentamer geometry is unable to stabilize a β -barrel conformation, it assumes various states instead, again in accordance with the experimental results which do not indicate a well defined structure for the pentameric interface; and (iii) atomistic simulations of the backmapped CG structures remain relatively stable, indicative of plausible CG conformations and slow kinetics on the atomistic level.