Free-energy calculations - Theoretical Biophysics Group

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Reaction coordinate–based free-energy calculations The algorithm 52 DARVE, POHORILLE (2001); HÉNIN, CHIPOT (2004); CHIPOT, HÉNIN (2005) 53 LELIÈVRE ET AL. (2007) Accrue the instantaneous force exerted along ξ in bins of finite size, δξ, and provide an estimate of dA(ξ)/dξ. The biasing force, − Fξ ∇ξ, is applied af- ξ ter a user-defined number of steps. ABF erases the roughness of the free energy surface along ξ. The system is in principle driven only by its self–diffusion properties, granted that ξ is essentially decoupled from the slow manifolds. 52 ABF formally converges. 53 Chris Chipot Free-energy calculations
Reaction coordinate–based free-energy calculations The algorithm 52 DARVE, POHORILLE (2001); HÉNIN, CHIPOT (2004); CHIPOT, HÉNIN (2005) 53 LELIÈVRE ET AL. (2007) Accrue the instantaneous force exerted along ξ in bins of finite size, δξ, and provide an estimate of dA(ξ)/dξ. The biasing force, − Fξ ∇ξ, is applied af- ξ ter a user-defined number of steps. ABF erases the roughness of the free energy surface along ξ. The system is in principle driven only by its self–diffusion properties, granted that ξ is essentially decoupled from the slow manifolds. 52 ABF formally converges. 53 Chris Chipot Free-energy calculations
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Free-energy calculations Measuring
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Foreword Free-energy differences ca
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Free-energy perturbation calculatio
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6 JORGENSEN, RAVIMOHAN (1985) 7 SIM
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8 WIDOM (1963) Free-energy perturba
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Substitute where Free-energy pertur
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Substitute where Free-energy pertur
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P(∆U ) 2.4 2.0 1.6 1.2 0.8 P (∆
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11 HUMMER ET AL. (1996) 12 HÜNENBE
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15 KIRKWOOD (1935) Free-energy pert
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16 PEARLMAN, KOLLMAN (1989) Free-en
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(a) 2.4 P(∆U ) 2.0 1.6 1.2 0.8 P
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(a) 2.4 P(∆U ) 2.0 1.6 1.2 0.8 P
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Page 49 and 50: 22 POHORILLE ET AL. (2010) Free-ene
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Page 57 and 58: protein + ligand 0 ∆ Aannihilatio
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Page 109 and 110: References BENNETT, C. H. (1976): E
Page 111 and 112: References KARLSSON, R.;LARSSON, A.
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