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Ala-5 Ramachandran maps. (A) Free energy surface G(ϕ,ψ) = −ln p(ϕ, ψ) from MD simulation with the AMBER99SB*-ildn-q force field averaged over the central residues 2–4. (B) Ramachandran plot for Ala residues outside of regular secondary structure from the PDB.11 (C) Free energy surface for the optimal BioEn ensemble with DFT2 Karplus parameters. (D) Free energy differences between initial ensemble and the optimal BioEn ensemble.
