Free-energy calculations - Theoretical Biophysics Group

More documents

Recommendations

Info

Free-energy perturbation calculations A pictorial representation of free-energy perturbation Important regions are volumes that encompass configurations of the system with highly probable energy values. A configuration in the important region should have the potential energy, the probability of which is higher than a given, predefined value. Configurations that belong to the important regions are expected to make significant contributions to the free energy and ought to be adequately sampled. Chris Chipot Free-energy calculations
(a) 2.4 P(∆U ) 2.0 1.6 1.2 0.8 P 1 (∆U ) 0.4 1 0.0 -1.2 -0.8 -0.4 0 0.4 0.8 1.2 1.6 (b) 2.4 ∆U P(∆U ) 2.0 1.6 1.2 0.8 0.4 P 1 (∆U ) Free-energy perturbation calculations A pictorial representation of free-energy perturbation P 0 (∆U ) P 0 (∆U ) 0.0 -1 -0.8 -0.6 -0.4 -0.2 0 0.2 0.4 0.6 ∆U (c) 2.4 P(∆U ) 2.0 1.6 1.2 P 1 (∆U ) 0.8 no sampling 0.4 P 0 (∆U ) 0.0 -1 -0.8 -0.6 -0.4 -0.2 0 ∆U (d) 2.4 0 0.2 0.4 0.6 2.0 i P (∆U ) 1 1.6 1.2 1 P (∆U ) 0 P(∆U ) 0.8 1 1 0 0 0.4 P(∆U ) i,i+1 0.0 -1.2 -0.8 -0.4 0 ∆U 0.4 0.8 1.2 18 LU, KOFKE (2001) 0 A pictorial representation of the relationship between the reference and the target systems may constitute a useful tool to detect inaccuracies caused by incomplete sampling. 18 If the important region of the target system fully overlaps, or is a subset of the important region of the reference system, P0(∆U) estimated from FEP calculations should be reliable. Good sampling of the important region in the reference system will also yield good sampling of the important region in the target system. If the important regions of the two systems do not overlap, the important region of the target state is not expected to be sufficiently sampled during a simulation of the reference system. Satisfactory estimates of ∆A are unlikely to be obtained. 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 and 38: 16 PEARLMAN, KOLLMAN (1989) Free-en
Page 39: Free-energy perturbation calculatio
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 91 and 92:
Reaction coordinate-based free-ener
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?