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. Author manuscript; available in PMC: 2012 Oct 1.
Published in final edited form as: J Comput Chem. 2011 Jul 6;32(13):2909–2923. doi: 10.1002/jcc.21876

Table 5.

Overall measures of model quality (in kcal/mol) for absolute hydration free energy predictions for trajectories analyzed using different implicit solvent models and common values for the nonpolar parameters.

Implicit solvent model: TC OBC OBC2 GBMV GBMV2 GBSW GBSW/MS GBSW/MS2 FACTS TIP3P
γ=0.005 kcal/(molA2); β=0.92 kcal/mol
<|Error|> 1.33 1.45 1.31 1.19 1.26 1.06 1.58 2.54 1.68 1.03
<Error> -0.48 -0.91 -0.44 0.45 0.55 0.03 -1.33 -2.43 1.26 0.67
RMS Error 1.93 2.18 1.93 1.56 1.62 1.38 2.09 3.23 2.18 1.26
R2 0.750 0.719 0.708 0.809 0.784 0.796 0.786 0.777 0.663 0.888
% |Error|<3 kcal/mol 90 88 90 94 93 96 89 67 85 99
% |Error|<2 kcal/mol 75 74 76 83 82 88 73 49 65 92
% |Error|<1 kcal/mol 53 54 54 52 48 57 39 22 38 51
Comparison with TIP3P
<|Diff|> 1.44 1.71 1.36 0.78 0.71 0.99 2.09 3.10 1.14
<Diff> -1.15 -1.59 -1.11 -0.22 -0.12 -0.64 -2.00 -3.10 0.58
R2 0.832 0.863 0.842 0.906 0.910 0.912 0.909 0.892 0.809
γ=0.005 kcal/(molA2); β=0 kcal/mol
<|Error|> 1.81 2.11 1.77 1.15 1.14 1.32 2.33 3.40 1.25 1.03
<Error> -1.50 -1.94 -1.47 -0.60 -0.50 -0.92 -2.28 -3.38 0.23 0.67
RMS Error 2.40 2.78 2.38 1.61 1.60 1.66 2.79 4.00 1.80 1.26
R2 0.750 0.718 0.708 0.809 0.784 0.797 0.786 0.777 0.663 0.888
% |Error|<3 kcal/mol 81 76 81 93 94 95 75 51 91 99
% |Error|<2 kcal/mol 67 63 69 85 84 77 45 25 83 92
% |Error|<1 kcal/mol 33 27 38 59 58 45 15 8 53 51
Comparison with TIP3P
<|Diff|> 2.27 2.66 2.24 1.40 1.29 1.68 2.95 4.05 1.04
<Diff> -2.17 -2.61 -2.14 -1.27 -1.17 -1.59 -2.95 -4.05 -0.44
R2 0.833 0.863 0.843 0.908 0.911 0.913 0.910 0.892 0.812
γ=0 kcal/(molA2); β=0 kcal/mol
<|Error|> 2.86 3.24 2.82 2.26 2.17 1.52 2.64 3.73 1.60 1.03
<Error> -2.77 -3.21 -2.73 -2.21 -2.10 -1.27 -2.62 -3.72 -1.08 0.67
RMS Error 3.37 3.80 3.34 2.67 2.61 1.87 3.08 4.31 2.12 1.26
R2 0.740 0.706 0.697 0.807 0.778 0.800 0.790 0.781 0.650 0.888
% |Error|<3 kcal/mol 63 58 67 76 79 93 67 44 92 99
% |Error|<2 kcal/mol 34 23 34 46 51 73 36 18 69 92
% |Error|<1 kcal/mol 10 6 10 16 22 36 12 5 38 51
Comparison with TIP3P
<|Diff|> 3.48 3.90 3.46 2.89 2.78 1.99 3.29 4.39 1.88
<Diff> -3.44 -3.88 -3.40 -2.88 -2.78 -1.94 -3.29 -4.39 -1.75
R2 0.835 0.862 0.843 0.923 0.922 0.914 0.912 0.895 0.825