Free-energy calculations - Theoretical Biophysics Group

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Free-energy perturbation calculations The perturbation formalism N–particle reference system described by Hamiltonian H0(x, px), function of 3N Cartesian coordinates, x, and conjugated momenta px. Goal: Calculate the free energy difference between the reference system and the target system characterized by Hamiltonian H1(x, px): H1(x, px) = H0(x, px) + ∆H (x, px) Example: Free energy of solvation of a chemical species at infinite dilution. ∆H (x, px) then consists of all terms in H1(x, px) that describe solute-solvent interactions. Example: Calculate the difference between the hydration free energies of sodium and argon described as Lennard–Jones particles with and without a charge. Chris Chipot Free-energy calculations
Free-energy perturbation calculations The perturbation formalism N–particle reference system described by Hamiltonian H0(x, px), function of 3N Cartesian coordinates, x, and conjugated momenta px. Goal: Calculate the free energy difference between the reference system and the target system characterized by Hamiltonian H1(x, px): H1(x, px) = H0(x, px) + ∆H (x, px) Example: Free energy of solvation of a chemical species at infinite dilution. ∆H (x, px) then consists of all terms in H1(x, px) that describe solute-solvent interactions. Example: Calculate the difference between the hydration free energies of sodium and argon described as Lennard–Jones particles with and without a charge. Chris Chipot Free-energy calculations
Page 1 and 2: Free-energy calculations Measuring
Page 3 and 4: Foreword Free-energy differences ca
Page 9 and 10: Free-energy perturbation calculatio
Page 11: 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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33 BEUTLER ET AL. (1994) 34 ZACHARI
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Free-energy perturbation calculatio
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36 POHORILLE ET AL. (2010) 37 LU ET
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Foreword Free-energy differences ca
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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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