Free-energy calculations - Theoretical Biophysics Group

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Free-energy perturbation calculations One simple application of perturbation theory An uncharged Lennard–Jones particle immersed in a large container of water acquires a charge q. The free energy change associated with charging is given by the forward FEP equation, in which state 0 refers to the reference state of the solvated Lennard–Jones sphere. Electrostatic energy of interaction between charge q and all water molecules: ∆U = qV V is the electrostatic potential created by the solvent and acting on the charge in the center of the cavity. Chris Chipot Free-energy calculations
Free-energy perturbation calculations One simple application of perturbation theory Second-order perturbation theory: ∆A = q〈V〉0 − β q2 (V − 〈V〉 0 ) 2 2 0 If water is considered as a homogeneous dipolar liquid, 〈V〉 0 = 0, the expression for the free energy change further simplifies to: ∆A = − β q2 V 2 2 0 This result implies that ∆A should be a quadratic function of the ionic charge. Chris Chipot Free-energy calculations
Page 1 and 2: Free-energy calculations Measuring
Page 3 and 4: Foreword Free-energy differences ca
Page 9 and 10: Free-energy perturbation calculatio
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
Page 23 and 24: Substitute where Free-energy pertur
Page 25 and 26: P(∆U ) 2.4 2.0 1.6 1.2 0.8 P (∆
Page 27: Free-energy perturbation calculatio
Page 31 and 32: 11 HUMMER ET AL. (1996) 12 HÜNENBE
Page 35 and 36: 15 KIRKWOOD (1935) Free-energy pert
Page 37 and 38: 16 PEARLMAN, KOLLMAN (1989) Free-en
Page 41 and 42: (a) 2.4 P(∆U ) 2.0 1.6 1.2 0.8 P
Page 43 and 44: (a) 2.4 P(∆U ) 2.0 1.6 1.2 0.8 P
Page 45 and 46: (a) 2.4 P(∆U ) 2.0 1.6 1.2 0.8 P
Page 49 and 50: 22 POHORILLE ET AL. (2010) Free-ene
Page 55 and 56: protein + ligand 0 ∆ Aannihilatio
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Page 63 and 64: 33 BEUTLER ET AL. (1994) 34 ZACHARI
Page 67 and 68: 36 POHORILLE ET AL. (2010) 37 LU ET
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Reaction coordinate-based free-ener
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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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