Free-energy calculations - Theoretical Biophysics Group

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Reaction coordinate–based free-energy calculations Bridging biological and computational time scales Chris Chipot Free-energy calculations
Reaction coordinate–based free-energy calculations A host of methods Umbrella sampling TORRIE, VALLEAU (1977) Constrained MD CARTER ET AL. (1989) DEN OTTER, BRIELS (2000) Non-equilibrium MD JARZYNSKI (1997) PARK (2003) Adaptive umbrella sampling BARTELS, KARPLUS (1998) Local elevation/flooding HUBER (1994) GRUBMÜLLER (1995) Adaptive biasing force DARVE, POHORILLE (2001) HÉNIN, CHIPOT (2004) MINOUKADEH ET AL. (2010) Metadynamics LAIO, PARRINELLO (2002) Adaptively biased MD BABIN ET AL. (2008) Degree of evolution DE DONDER (1927) Generalized extent parameter KIRKWOOD (1935) Commitment probability ONSAGER (1938) Minimum-resistance path BERKOWITZ ET AL. (1983) Minimum-action path OLENDER, ELBER (1996) FRANKLIN (2007) Transition path sampling BOLHUIS ET AL. (2002) String method E ET AL. (2002) PAN ET AL. (2008) Milestoning FARADJIAN (2004) Maximum flux transition path ZHAO ET AL. (2010) Chris Chipot Free-energy calculations
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Free-energy calculations Measuring
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Foreword Free-energy differences ca
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Free-energy perturbation calculatio
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6 JORGENSEN, RAVIMOHAN (1985) 7 SIM
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8 WIDOM (1963) Free-energy perturba
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Substitute where Free-energy pertur
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Substitute where Free-energy pertur
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P(∆U ) 2.4 2.0 1.6 1.2 0.8 P (∆
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Page 31 and 32: 11 HUMMER ET AL. (1996) 12 HÜNENBE
Page 33 and 34: Free-energy perturbation calculatio
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
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Page 49 and 50: 22 POHORILLE ET AL. (2010) Free-ene
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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Page 109 and 110: References BENNETT, C. H. (1976): E
Page 111 and 112: References KARLSSON, R.;LARSSON, A.
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Free-energy calculations - Theoretical Biophysics Group

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