Free-energy calculations - Theoretical Biophysics Group

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39 BENNETT (1976) Free-energy perturbation calculations Improving the efficiency of FEP calculations It requires that one forward and one backward calculation be performed at every intermediate state. Additional intermediate does not have to be located at λi + ∆λ/2, but, instead, may be chosen at any value comprised between λi and λi + ∆λ. Ideally, the location of the intermediate should be found to minimize the statistical error of ∆Ai,i+1. 39 Chris Chipot Free-energy calculations
Free-energy perturbation calculations Improving the efficiency of FEP calculations This is tantamount to calculating 1 + exp[β(∆Ui,i+1 − C)] −1 exp(−β∆Ai,i+1) = i {1 + exp[−β(∆Ui,i+1 − C)]} −1 i+1 × exp(−βC) C is a constant that determines the position of the additional intermediate, C = ∆Ai,i+1 + 1 ni ln β ni+1 C cannot be accessed directly because it involves the unknown value of ∆Ai,i+1. Instead, the equations for exp(−β∆Ai,i+1) and C are solved iteratively at a post– processing stage. 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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Page 19 and 20: 8 WIDOM (1963) Free-energy perturba
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
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
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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
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Page 63 and 64: 33 BEUTLER ET AL. (1994) 34 ZACHARI
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Page 109 and 110: References BENNETT, C. H. (1976): E
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Free-energy calculations - Theoretical Biophysics Group

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