Figure 17.

(a) Energy change during formation of the second kink (sites Asn22-Ile32) of protein A in a generic UNRES simulation. The fluctuations in the average value of energy are consistently around 7 kcal/mol. The kink formation takes place very rapidly during a small number of UNRES steps. Between steps ≈ 620 and 800, the second kink drifts towards the first kink, causing the energy to drop on average of about 3 kcal/mol. (b) The average energy between the first two kinks increases by an amount that is comparable to the decrease in average energy in (a). The change is due to oscillation in the distance between the two kinks; the second one drifts towards the first one, causing the energy to increase.