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. Author manuscript; available in PMC: 2008 Oct 20.
Published in final edited form as: J Am Chem Soc. 2006 Oct 4;128(39):12766–12777. doi: 10.1021/ja060830y

Figure 2.

Figure 2

Representation of the convergence of entropy calculations using the quasi-harmonic approximation. (a) Entropy (TS) of the NHERF PDZ domain apo (black line) and holo in complex with the ‘b’ peptide (grey line) calculated on cumulative blocks, starting at 5 ns of MD simulations on intervals increasing by 0.5 ns. (b) Entropy part of the binding free energy (see Methods) calculated on cumulative blocks for the NHERF PDZ domain in complex with the ‘b’ peptide.