Figure 3.

Final 1 ns averaged loop structures of some models after 50 ns MD simulations. (a) T-L_n, (b) T₃-L_n, (c) TTA-L_w, (d) T₃-P₃a, (e) T-P₄a (the stem residue adjacent to the 3′-end of the loop is also shown in color), (f) 0-P₃p (the two directly connected stem residues are shown in color), (g) T₄-L_w-3, and (h) T₄-L_w-2. The loops are shown as colored tubes, and the terminal quartets or stems are shown as black lines. The loop direction follows Figure 2, and the residue numbers are not labeled.