The graph above is for the PM6 model.

The difference in free energy for PHE is -2.7 kcal mol-1

The difference in free energy for TRP is -4.0 kcal mol-1

Question 4.1 - The graphs of energy versus λ are completely straight lines. The energy scales linearly from the QM energy to the MM energy. In contrast, the PMFs above are very slightly curved. The value at λ = 1 is also less negative (-2.7 compared to -3.2 for PHE and -4.0 compared to -4.2 for TRP).

Question 4.2 - The free energy difference is more negative than the average energy difference calculated in exercise 2 for PHE (-2.7 compared to -2.2), but less negative for TRP (-4.0 compared to -4.3).

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