Free-energy calculations - Theoretical Biophysics Group

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10 BORN (1920) Free-energy perturbation calculations One simple application of perturbation theory Born model: The ion is a spherical particle of radius a and the solvent is represented as a dielectric continuum characterized by a dielectric constant ε: 10 ε − 1 ∆A = − ε q 2 2a Comparison between prediction and computer simulations requires care. In practice, the computed values of ∆A exhibit considerable system–size dependence, i.e. they vary with the size of the simulation box, because charge–dipole interactions between the solute and solvent molecules decay slowly as 1/r 2 . Chris Chipot Free-energy calculations
11 HUMMER ET AL. (1996) 12 HÜNENBERGER, MCCAMMON (1999) Free-energy perturbation calculations One simple application of perturbation theory System–size effects can be greatly reduced by properly correcting for the self–interaction term, which is due to interactions between the charge and its images and the neutralizing background. 11 This is true for both Ewald lattice summation and generalized reaction field treatments of finite–size effects. 12 In general, free energy calculations, in which the system is transformed such that its electrical charge changes, should include system–size corrections. Chris Chipot Free-energy calculations
Page 1 and 2: Free-energy calculations Measuring
Page 3 and 4: Foreword Free-energy differences ca
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Page 11 and 12: 6 JORGENSEN, RAVIMOHAN (1985) 7 SIM
Page 19 and 20: 8 WIDOM (1963) Free-energy perturba
Page 21 and 22: Substitute where Free-energy pertur
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Page 25 and 26: P(∆U ) 2.4 2.0 1.6 1.2 0.8 P (∆
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Page 35 and 36: 15 KIRKWOOD (1935) Free-energy pert
Page 37 and 38: 16 PEARLMAN, KOLLMAN (1989) Free-en
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Good practices Free-energy perturba
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References BENNETT, C. H. (1976): E
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References KARLSSON, R.;LARSSON, A.
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Free-energy calculations - Theoretical Biophysics Group

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