Free-energy calculations - Theoretical Biophysics Group

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m c / (kJ mol −1 ) 1000 800 600 400 200 0 −200 −400 −600 −1 −0.5 0 q / e 0.5 1 13 HUMMER ET AL. (1996) 14 MARKUS (1991) Free-energy perturbation calculations One simple application of perturbation theory EW, N=256 GRF, N=256 EW, N=128 fit Monte Carlo simulations, in which a non-polar particle is progressively charged to q = 1 or q = −1 in intervals of 0.25 e, indicated that the predicted quadratic dependence of ∆A on q is essentially correct. 13 In agreement with experimental data 14 negative ions are, however, better hydrated than positive ions, reflected by the different slopes of the straight line. This can be ascribed to different arrangements of water molecules in the vicinity of the ion. The positively charged hydrogen atoms of water, which possess small van der Waals radii, can approach negative ions closer than large, negative oxygen atoms approach positive ions. Chris Chipot Free-energy calculations
Free-energy perturbation calculations How to deal with large perturbations? Direct use of the forward FEP equation can be successful only if P0(∆U) is a narrow function of ∆U. This does not imply that the free energy difference between the reference and the target states must be small. Example: Although the hydration free energy of benzene is only −0.767 kcal/mol at 298 K, this quantity cannot be successfully calculated by direct application of the FEP equation to a simulation of a reasonable length, because low–energy configurations in the target ensemble, which do not suffer from the overlap between the solute and solvent molecules, are not sampled in simulations of the reference state. 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 31: 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
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Page 45 and 46: (a) 2.4 P(∆U ) 2.0 1.6 1.2 0.8 P
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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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