Figure 13.

The initial conformation in Figure 12 is a local minimum conformation while the kink, i.e., loop, forms between two such local minima (a and b). If another initial conformation is chosen, for example, polyproline-II, these correspond to unstable states such as conformation c shown in the figure. This will cause initial conformation-specific embryonic fluctuations around the local minimum. But, already during the very early stages of the folding process, these random fluctuations become mingled with thermal fluctuations and lose their relevance in guiding the folding process. In specifying the initial conformations in our simulations, we try to minimize transient random effects.