Figure 3.

Equilibration and stability of the folded PIN2 helix clusters. (A) System temperature of part 1 (left) and part 3 (right) over the full production run. The raw data are in black, while the red and blue lines show window averages over 10 and 100 ps, respectively; (B) Potential energy (green), kinetic energy (red) and total energy (black) of part 1 (left) and of part 3 (right) over the same period as in (A); (C) RMSD of the lowest-energy conformation of part 1 (left) and part 3 (right) with respect to every other frame in the simulation, after alignment (black); the red and light blue lines are window averages over periods of 20 and 200 ps, respectively.