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. Author manuscript; available in PMC: 2009 Jan 28.
Published in final edited form as: J Chem Theory Comput. 2008 Oct 14;4(10):1669–1680. doi: 10.1021/ct8002173

Table 1.

Free Energies for Transitions between Two Values, ν and η, of Various Dihedral Angles in the Seryl-Serine Systema

dihedral angle ν (deg) η (deg) 〈ΔG 〈|ΔΔG|〉 (2.5 × 104) 〈|ΔΔG|〉 (105) 〈|ΔΔG|〉 (106)
residue 1, χ1 −123 −76 −2.07 ± 0.01 0.37 ± 0.25 0.28 ± 0.18 0.10 ± 0.07
residue 2, χ2 120 −120 −1.42 ± 0.02 0.31 ± 0.16 0.32 ± 0.17 0.07 ± 0.07
residue 1, ψ 107 −29 1.72 ± 0.04 0.47 ± 0.31 0.20 ± 0.11 0.14 ± 0.14
residue 2, ϕ 43 105 −0.04 ± 0.01 0.11 ± 0.09 0.08 ± 0.08 0.03 ± 0.02
residue 2, ϕ 105 231 −1.27 ± 0.05 0.77 ± 0.50 0.70 ± 0.50 0.20 ± 0.11
residue 2, ϕ 43 231 −1.31 ± 0.06 0.74 ± 0.48 0.69 ± 0.52 0.21 ± 0.12
a

The chosen values of ν and η correspond to relative maxima indentified in the unbiased ensemble (see Figure 6) generated with an infinite sequence of Langevin forces. ΔG values, reported with standard deviations in kcal/mol, refer to the transition free energy for the unbiased ensemble (see eq 6); angular brackets 〈 〉 refer to averages from eight independent trajectories. Similarly, |ΔΔG| values refer to absolute changes in the transition free energy if a finite sequence of Langevin forces (of length specified in parentheses) is used (see eq 7).