Free-energy calculations - Theoretical Biophysics Group

More documents

Recommendations

Info

Reaction coordinate–based free-energy calculations A vector field approach Derivative of the free energy with respect to the order parameter: dA(ξ) dξ = − 1 β 1 Q(ξ) dQ(ξ) dξ Partition function: Q(ξ) = δ[ξ − ξ(x)] exp[−βU(x)] dx The δ–function can be viewed as a square pulse of width ∆ξ. Q(ξ) is an integral over a thin slab of configurational space, i.e. a sum of the Boltzmann weight over the volume elements vi(ξ), so that: Q(ξ) = 1 ∆ξ exp[−βUi(ξ)] vi(ξ) i Chris Chipot Free-energy calculations
Reaction coordinate–based free-energy calculations A vector field approach Increase the order parameter by δξ. The partition function, Q(ξ +δξ), is obtained from summing all volume elements in the new slab bounded by surfaces ξ(x) = ξ + δξ ± 1/2∆ξ: Q(ξ + δξ) = 1 ∆ξ exp[−βUi(ξ + δξ)] vi(ξ + δξ) i Assuming that the changes in the volume elements is sufficiently small, δQ(ξ) can be approximated from a Taylor expansion: δQ(ξ) δξ = 1 ∆ξ −β i δUi(ξ) 1 δvi(ξ) + δξ vi(ξ) δξ × exp[−βUi(ξ)] vi(ξ) Chris Chipot Free-energy calculations
Page 1 and 2:
Free-energy calculations Measuring
Page 3 and 4:
Foreword Free-energy differences ca
Page 5 and 6:
Page 7 and 8:
Page 9 and 10:
Free-energy perturbation calculatio
Page 11 and 12:
6 JORGENSEN, RAVIMOHAN (1985) 7 SIM
Page 13 and 14:
Page 15 and 16:
Page 17 and 18:
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 and 28:
Page 29 and 30:
Page 31 and 32:
11 HUMMER ET AL. (1996) 12 HÜNENBE
Page 33 and 34:
Page 35 and 36:
15 KIRKWOOD (1935) Free-energy pert
Page 37 and 38:
16 PEARLMAN, KOLLMAN (1989) Free-en
Page 39 and 40:
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 47 and 48: Free-energy perturbation calculatio
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 77 and 78: Foreword Free-energy differences ca
Page 79 and 80: Reaction coordinate-based free-ener
Page 91: Reaction coordinate-based free-ener
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

Create successful ePaper yourself

Delete template?

Save as template?