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. Author manuscript; available in PMC: 2013 Jul 14.
Published in final edited form as: J Phys Chem B. 2009 Jul 23;113(29):9728–9740. doi: 10.1021/jp9020646

FIG. 10.

FIG. 10

Dependence of the confinement results on the definition of the free-energy basins corresponding to the investigated molecular states. Here, the data refer to bhp1 and bhp2 states of the β-hairpin peptide. On top, are shown the calculated ΔGAB values (i.e., ΔGbhp2 – ΔGbhp1) as a function of the RMSD cutoff used in the analysis. On bottom, are shown the free-energy projections of the individual basins of the β-hairpin peptide (see Ref. [31]) on the Cα-RMSD from the reference structure of both bhp1 (left) and bhp2 (right) states. The free-energy profiles were generated from the histograms of the Cα-RMSD computed for each basin from the structural ensembles sampled by equilibrium MD at 360 K and kinetically partitioned as described in Ref. [31].