Free-energy calculations - Theoretical Biophysics Group

More documents

Recommendations

Info

Free-energy perturbation calculations A pictorial representation of free-energy perturbation In FEP calculations, configurations are sampled according to the probability, P0(U), of finding the reference system in a state corresponding to the potential energy U. Does it guarantee that the key quantity for calculating ∆A, i.e. P0(∆U), is estimated accurately? Unfortunately, this does not have to be the case. FEP will only provide accurate estimates of free energy differences under the sine qua non condition that the target system be sufficiently similar to the reference system. Chris Chipot Free-energy calculations
Free-energy perturbation calculations A pictorial representation of free-energy perturbation In FEP calculations, configurations are sampled according to the probability, P0(U), of finding the reference system in a state corresponding to the potential energy U. Does it guarantee that the key quantity for calculating ∆A, i.e. P0(∆U), is estimated accurately? Unfortunately, this does not have to be the case. FEP will only provide accurate estimates of free energy differences under the sine qua non condition that the target system be sufficiently similar to the reference system. 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 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: 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 79 and 80: Reaction coordinate-based free-ener
Page 89 and 90:
Reaction coordinate-based free-ener
Page 91 and 92:
Page 93 and 94:
Page 95 and 96:
Page 97 and 98:
Page 99 and 100:
Page 101 and 102:
Page 103 and 104:
Page 105 and 106:
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

You also want an ePaper? Increase the reach of your titles

Delete template?

Save as template?