Free-energy calculations - Theoretical Biophysics Group

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Free-energy perturbation calculations Measuring the error associated to an FEP calculation In simulations of finite length, where regions contributing significantly to the free-energy difference are ignored, only the second term obviously prevails. +∞ exp(−β∆A0) = P0(∆U) exp(−β∆U) d∆U ∆U 0 The systematic error is the difference between the exact free-energy difference and its finite-sampling biased estimator, δɛ 0 ∆U0 = − bias,∆A −∞ P0(∆U) exp(−β∆U) d∆U Of practical interest is the relative systematic error associated to the measure of the forward free-energy difference, δɛ0 ∆U0 bias,∆A = − exp(−β∆A) −∞ Chris Chipot Free-energy calculations P1(∆U) d∆U
Foreword Free-energy differences can be estimated computationally following four different routes: Methods based on histograms, 44 Non-equilibrium work simulations, 45 Perturbation theory, 46 Measuring the derivative and integrating it. 47 44 WIDOM (1963); TORRIE, VALLEAU (1977) 45 JARZYNSKI (1997); IZRAILEV ET AL. (1998); CROOKS (1999) 46 LANDAU (1938); ZWANZIG (1954); BENNETT (1976) 47 KIRKWOOD (1935); CARTER ET AL. (1989); WIDOM (1963) 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
Page 25 and 26: P(∆U ) 2.4 2.0 1.6 1.2 0.8 P (∆
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Page 31 and 32: 11 HUMMER ET AL. (1996) 12 HÜNENBE
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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
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Page 67 and 68: 36 POHORILLE ET AL. (2010) 37 LU ET
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Free-energy calculations - Theoretical Biophysics Group

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