Free-energy calculations - Theoretical Biophysics Group

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Free-energy perturbation calculations “Alchemical transformations” The concept of order parameter is central to free energy calculations: They are collective variables used to describe transformations from the initial, reference system to the final, target one. An order parameter may, albeit does not necessarily have to correspond to the path along which the transformation takes place in nature, and would be called the reaction coordinate or the reaction path if such were the case. There is more than one way to define an order parameter. How to make the best, or at least an appropriate, choice of an order parameter? The choice of order parameters may have a significant effect on the efficiency and accuracy of free energy calculations. Some order parameters may map a smooth path between the reference and target states whereas others may lead through a rough energy landscape. Chris Chipot Free-energy calculations
22 POHORILLE ET AL. (2010) Free-energy perturbation calculations “Alchemical transformations” Central to the application of FEP to alchemical transformations is the concept of a thermodynamic cycle. The cycle may be hypothetical, as individual transformations can be carried out only on the computer. Considering that all transformations are reversible, the cycle can be run in both directions and the free energy of interest can be calculated from either forward or backward transformations. The computational efficiencies of carrying out these transformations may, however, differ. 22 Chris Chipot Free-energy calculations
Page 1 and 2: Free-energy calculations Measuring
Page 3 and 4: Foreword Free-energy differences ca
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Page 11 and 12: 6 JORGENSEN, RAVIMOHAN (1985) 7 SIM
Page 19 and 20: 8 WIDOM (1963) Free-energy perturba
Page 21 and 22: Substitute where Free-energy pertur
Page 23 and 24: Substitute where Free-energy pertur
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
Page 43 and 44: (a) 2.4 P(∆U ) 2.0 1.6 1.2 0.8 P
Page 45 and 46: (a) 2.4 P(∆U ) 2.0 1.6 1.2 0.8 P
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Page 55 and 56: protein + ligand 0 ∆ Aannihilatio
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Page 63 and 64: 33 BEUTLER ET AL. (1994) 34 ZACHARI
Page 67 and 68: 36 POHORILLE ET AL. (2010) 37 LU ET
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Reaction coordinate-based free-ener
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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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