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We note that the comment includes a list of some differences in the simulation setups: these and other differences in the two sets of setups need to be investigated as possible contributors to the difference in the simulation results. Such an approach appears to assume that water outside this artificial volume behaves as bulk water which is not evident. The water-water hydrogen bond network reconfigures when the structure of the protein changes T vs.

Following a transition in the protein structure these changes occur on the few nanosecond time scale, as a direct response to the protein structure change. This suggests that the protein and water dynamics are coupled and can not be viewed independently.

As an important test we have solvated the decayed i. Apparently, solvation of the decayed structure in the larger water box provides the driving force required to partially recover the T 0 structure.

Chemistry The Molecular Nature of Matter and Change Solutions Manual

This is an additional indication that, thermodynamically, T 0 is favored over R 0 in the largest water box without, however, providing information concerning a quantitative measure of the underlying energetics. Full recovery would require much longer simulations. Technically, it is desirable to carry out simulations in a setup that allows the solvent — here water — to behave as a pure liquid for quantities such as g r or the average number of H-bonds.


The normalization procedure of the radial distribution functions used in the comment remains unclear. It should be noted that the radial distribution functions in El Hage et al.

Figure 5 in El Hage et al. Kinetics as a function of box size This section raises questions as to the statistical significance of the results.

As mentioned above and in Figure 2 , converged reaction time distributions require hundreds to thousands of transitions. Bookmark it to easily review again before an exam.

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