Free-energy calculations - Theoretical Biophysics Group

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Free-energy perturbation calculations How to deal with large perturbations? The difficulty in applying FEP theory can be circumvented through a stratification strategy, or staging. It relies on constructing several intermediate states between the reference and the target state such that P(∆Ui,i+1) for two consecutive states i and i+1 sampled at state i is sufficiently narrow for the direct evaluation of the corresponding free energy difference, ∆Ai,i+1. With N−2 intermediate states, N−1 ∆A = i=1 ∆Ai,i+1 = − 1 β N−1 i=1 Chris Chipot Free-energy calculations ln exp −β∆Ui,i+1 i
15 KIRKWOOD (1935) Free-energy perturbation calculations How to deal with large perturbations? Intermediate states do not need to be physically meaningful, i.e. they do not have to correspond to systems that actually exist. More generally, the Hamiltonian can be considered to be a function of some parameter, λ. Without loss of generality, λ can be defined between 0 and 1, such that λ = 0 and λ = 1 for the reference and target states, respectively. A simple choice for the dependence of the Hamiltonian on λ, the coupling parameter: 15 H (λi) = λiH1 + (1 − λi)H0 = H0 + λi∆H ∆H is the perturbation term in the target Hamiltonian, equal to H1 − H0. Chris Chipot Free-energy calculations
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Page 11 and 12: 6 JORGENSEN, RAVIMOHAN (1985) 7 SIM
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Page 21 and 22: Substitute where Free-energy pertur
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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
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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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