Figure 3.

Kinetics of H bonding. (a) Time dependence of the number of protein–protein hydrogen bonds n_pp(t) during the collapse of (Gly)_N for different N. To make the curves fall within the same scale, the data is normalized with n_pp(t_f); t_f is the maximum run time the simulations are done. The inset shows the time dependence of n_pp(t) for (Gly)₂₀. (b) Same as in panel (a) but for the number of protein–water hydrogen bonds n_pw(t). Here, the normalization is done with n_pw(0). The inset shows the variation of n_pw(t) with time for (Gly)₂₀. The error bars in all the plots here correspond to the standard error of the mean calculated while averaging the data obtained from a number (mentioned in the Model and Methods section) of independent simulations.