Figure 2.

Potential of mean force (PMF) as a function of the end-to-end distance for UUCG, obtained with different initial velocities using AMBER ff99. Solid: set 1; dotted: set 2; dashed: set 3. The structures shown along with the PMF are snapshots of structures sampled by the umbrella sampling simulation. Note that because the hairpin becomes more disordered at large end-to-end distance, a significantly larger ensemble was sampled than is suggested by these snapshots at large r. The sampled conformations are better represented by these snapshots at short end-to-end extensions.