Free-energy calculations - Theoretical Biophysics Group

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Reaction coordinate–based free-energy calculations Order parameters 48 BOLHUIS ET AL. (2002); E ET AL. (2005); ZHAO ET AL. (2010) The reaction coordinate is the committor function in R 3N , defined between 0 and 1. 48 The definition of order parameter ξ : R 3N → R n , with n small, is reasonable if ξ is essentially decoupled from the slow manifolds. The choice of an order parameter, or combination thereof, unlikely to embrace concerted, collective movements is prone to yield quasi non-ergodicity scenarios. Chris Chipot Free-energy calculations
Reaction coordinate–based free-energy calculations A backdrop on potential of mean force calculations Generalization of the classical definition of w(r), based on g(r), w(r) = −1/β ln g(r), is not straightforward. 49 Turn to an alternate definition: A(ξ) = − 1 β ln Pξ + A0 Probability to find the system at ξ along the order parameter: Pξ = δ[ξ − ξ(x)] exp[−βH (x, px)] dx dpx First derivative of the free energy with respect to the order parameter: dA(ξ) dξ = ∂H (x, px) ∂ξ ξ 49 CHANDLER (1987) 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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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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Free-energy calculations - Theoretical Biophysics Group

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