Free-energy calculations - Theoretical Biophysics Group

More documents

Recommendations

Info

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
Reaction coordinate–based free-energy calculations Synopsis 1 Free-energy perturbation calculations 2 Reaction coordinate–based free-energy calculations 3 Good practices Chris Chipot Free-energy calculations
Page 1 and 2:
Free-energy calculations Measuring
Page 3 and 4:
Foreword Free-energy differences ca
Page 5 and 6:
Page 7 and 8:
Page 9 and 10:
Free-energy perturbation calculatio
Page 11 and 12:
6 JORGENSEN, RAVIMOHAN (1985) 7 SIM
Page 13 and 14:
Page 15 and 16:
Page 17 and 18:
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 27 and 28: Free-energy perturbation calculatio
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
Page 49 and 50: 22 POHORILLE ET AL. (2010) Free-ene
Page 55 and 56: protein + ligand 0 ∆ Aannihilatio
Page 57 and 58: protein + ligand 0 ∆ Aannihilatio
Page 63 and 64: 33 BEUTLER ET AL. (1994) 34 ZACHARI
Page 67 and 68: 36 POHORILLE ET AL. (2010) 37 LU ET
Page 77: Foreword Free-energy differences ca
Page 81 and 82: Reaction coordinate-based free-ener
Page 107 and 108: Good practices Free-energy perturba
Page 109 and 110: References BENNETT, C. H. (1976): E
Page 111 and 112: References KARLSSON, R.;LARSSON, A.
show all

Free-energy calculations - Theoretical Biophysics Group

Create successful ePaper yourself

Delete template?

Save as template?