Molecular dynamics simulations were carried out for the human Sm proteins B and D-3, and two different configurations of their complexes, B/D-3 and D-3/B, to investigate the structures of possible subcomplexes used for assembly of the ring structure comprised of the seven Sm proteins. Comparison of the free energy for the two sub-complexes revealed that the D-3/B configuration, in which the beta4 strand of B interacts with the beta5 strand of D-3 protein, is energetically preferred relative to the B/D-3 configuration. The direct interaction energy in vacuo and the solvation energy provided the largest contributions to the free energy. The torsional low-frequency vibration modes provided the largest contribution to the entropic terms due to complex formation, although the single mode also gave a small contribution. Determining the configuration of the D-3/B sub-complex provides powerful support for a proposed binding mechanism of the Sm proteins on snRNA.