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. Author manuscript; available in PMC: 2011 Dec 14.
Published in final edited form as: J Phys Chem B. 2007 Jan 11;111(1):260–285. doi: 10.1021/jp065380a

Fig. 3.

Fig. 3

Illustration of the role of inclusion of the Shannon-entropy term in eq 25 in the last iteration of the optimization of the force field using 1GAB as the training protein (section 4.2). Left panels: linear plots of the dimensionless free energies (U/RT − ln ω) at T = 300 K (with ω defined by eq 15) of the conformations of the 1GAB protein at level 0 (filled circles), 1 (filled diamonds), 2 (filled triangles), and 3 (asterisks); the symbols are seen most clearly in panel b. Only the low-free-energy parts are shown for clarity, and the F/RT span is the same on all three panels for better comparison. Right panels: plots of partial dimensionless free energies calculated by taking only the N lowest-free-energy conformations (where N is the variable of the abscissa) sorted according to U/RT − ln ω. Solid lines: level 0; short-dashed lines: level 1; long-dashed lines: level 2; dash-dotted lines: level 3. (a) Before minimizing the target function, (b) After minimizing the target function without including the Shannon-entropy term. (c) After minimizing the target function with inclusion of the Shannon-entropy term.