b. Stem Distance. The RNA hairpin loop has specific hydrogen bonding pattern between two stem regions. Therefore, the center of the mass distance between the two stem regions helps monitoring the relative motions of the stem regions with respect to the loop part of the RNA. For the first stem, the part center of mass of the backbone and bases of residues 2, 3, and 4 were used. For the other stem region center of mass of the backbone and base of residues 9, 10, and 11 were considered.