Table 6.

Free energy differences and statistical errors (all the values are in kcal/mol). (a) Current simulations. The second column reports the total, the third the free energy difference in MPH1, the fourth the free energy difference in MPH2 and the fifth the long-range correction (LRC). (b) Solvation free energies of the ILE and GLN side chain analogs as reported in²³. The second column is total, the third the free energy difference while creating Van der Waals interactions between the solute and the solvent with the electrostatic interactions off (analogous to MPH1), the fourth column reports the free energy of creating electrostatic interactions when the Van der Waals are already ”on” (analogous to MPH2). The last column is the long-range correction (LRC). The protocol used to carry out these calculations in²³ is significantly different from ours. The authors in²³ carried out NPT simulations and their cutoff scheme is different (no Ewald summation for electrostatics, they used instead group-based and tapered interactions). This is reflected mostly in the LRC term, which depends on the scheme used for the Van der Waals cutoff. (c) Experimental results for the solvation free energies of the two side chain analogs³⁵. These results were used as a comparison with the simulations in²³.

a
	TOTAL	MPH1	MPH2	LRC
ΔFI-Q,solv	−14.073±0.066	−16.218±0.050	2.199±0.043	−0.051
ΔFI-Q,vac	−2.847±0.068	−10.931±0.047	8.084±0.049
ΔFI,solv	2.891±0.050	3.379±0.050	−0.0075±0.0019	−0.481
ΔFQ,solv	−8.354±0.054	1.858±0.047	−9.680±0.027	−0.532

b
	Total23	Vdw23	Ele23	LRC23
ΔFI,solv	2.73±0.03	3.10±0.03	−0.01±0.001	−0.37
ΔFQ,solv	−8.40±0.04	1.80±0.03	−9.79±0.02	−0.41

c
	Experiment23,35
ΔFI,solv	2.15
ΔFQ,solv	−9.38