Free-energy calculations - Theoretical Biophysics Group

More documents

Recommendations

Info

Free-energy perturbation calculations Interpretation of the free energy perturbation equation Since ∆A is calculated as the average over a quantity that depends only on ∆U, this average can be taken over the probability distribution P0(∆U) instead of P0(x, px): 9 ∆A = − 1 β ln exp (−β∆U) P0(∆U) d∆U If U0 and U1 were the functions of a sufficient number of identically distributed random variables, then ∆U would be Gaussian–distributed (CLT). In practice, the probability distribution P0(∆U) deviates somewhat from the ideal Gaussian case, but still has a “Gaussian–like” shape. The integrand, the probability distribution multiplied by the Boltzmann factor exp (−β∆U), is shifted to the left and, hence, depends on the low-energy tail. 9 SHING, GUBBINS (1982) Chris Chipot Free-energy calculations
Substitute where Free-energy perturbation calculations Interpretation of the free energy perturbation equation to the expression of ∆A. P0(∆U) = 1 2 ∆U − 〈∆U〉0 √ exp − 2πσ 2σ2 σ 2 = ∆U 2 0 − 〈∆U〉 2 0 A Gaussian P0(∆U) obviates the need to carry out a numerical integration: ∆A = 〈∆U〉 0 − 1 2 βσ2 This analytical expression of ∆A has a broader significance: The first term, which is simply equal to the average energy difference measured in the reference state, can be either positive or negative. The second term, which depends on fluctuations of ∆U, is always negative. 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: 8 WIDOM (1963) Free-energy perturba
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 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
Page 57 and 58: protein + ligand 0 ∆ Aannihilatio
Page 63 and 64: 33 BEUTLER ET AL. (1994) 34 ZACHARI
Page 67 and 68: 36 POHORILLE ET AL. (2010) 37 LU ET
Page 71 and 72:
Free-energy perturbation calculatio
Page 73 and 74:
Page 75 and 76:
Page 77 and 78:
Foreword Free-energy differences ca
Page 79 and 80:
Reaction coordinate-based free-ener
Page 81 and 82:
Page 83 and 84:
Page 85 and 86:
Page 87 and 88:
Page 89 and 90:
Page 91 and 92:
Page 93 and 94:
Page 95 and 96:
Page 97 and 98:
Page 99 and 100:
Page 101 and 102:
Page 103 and 104:
Page 105 and 106:
Page 107 and 108:
Good practices Free-energy perturba
Page 109 and 110:
References BENNETT, C. H. (1976): E
Page 111 and 112:
References KARLSSON, R.;LARSSON, A.
show all

Free-energy calculations - Theoretical Biophysics Group

You also want an ePaper? Increase the reach of your titles

Delete template?

Save as template?