Computing free energies and accelerating rare events with metadynamics

Lecture Notes in Physics

Volumn 703, Issue , 2006, Pages 315-347

  Laio, A ^a   Parrinello, M ^b  

^a SISSA   (Italy)

^b Computational Science ^*  (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 33947208885     PISSN: 00758450     EISSN: None     Source Type: Book Series    
DOI: 10.1007/3-540-35273-2_9     Document Type: Article

References (59)

1. W. E. and E. Vanden-Eijnden (2004) Metastability, conformation dynamics, and transition pathways in complex systems. Lecture notes in computational science and engineering, Ed. S. Attinger and P. Koumoutsakos, Springer Berlin Heidelberg
2. E. Carter, G. Ciccotti, J. Hynes, and R. Kapral (1989) Constrained reaction coordinate dynamics for the simulation of rare events. Chem. Phys. Lett. 156, p. 472
3. M. Sprik and G. Ciccotti (1998) Free energy from constrained molecular dynamics. J. Chem. Phys. 109, p. 7737
4. P. A. Bash, U. C. Singh, F. K. Brown, R. Langridge, and P. A. Kollman (1987) Free energy calculation by computer simulation. Science 235, pp. 574-576
5. G. N. Patey and J. P. Valleau (1975) Monte-carlo method for obtaining interionic potential of mean force in ionic solution. J. Chem. Phys. 63, pp. 2334-2339
6. A. Ferrenberg and R. Swendsen (1988) Optimized monte-carlo data-analysis. Phys. Rev. Lett. 61, p. 2635
7. S. Kumar, J. M. Rosenberg, D. Bouzida, R. H. Swendsen, and P. A. Kollman (1995) Multidimensional free-energy calculations using the weighted histogram analysis method. J. Comput. Chem. 16, pp. 1339-1350
8. B. Roux (1995) The calculation of the potential of mean force using computersimulations. Comput. Phys. Comm. 91, pp. 275-282
9. H. Merlitz and W. Wenzel (2002) Comparison of stochastic optimization methods for receptor-ligand docking. Chem. Phys. Lett. 362, pp. 271-277
10. C. Jarzynski (1997) Nonequilibrium equality for free energy differences. Phys. Rev. Lett. 78, p. 2690
11. E. Darve and A. Pohorille (2001) Calculating free energies using average force. J. Chem. Phys. 115, pp. 9169-9183
12. D. Rodriguez-Gomez, E. Darve, and A. Pohorille (2004) Assessing the efficiency of free energy calculation methods J. Chem. Phys. 120, p. 3563
13. L. Rosso, P. Minary, Z. Zhu, and M. Tuckerman (2002) On the use of the adiabatic molecular dynamics technique in the calculation of free energy profiles. J. Chem. Phys. 116, pp. 4389-4402
14. E. Weinan, W. Ren, and E. Vanden-Eijnden (2005) Finite temperature string method for the study of rare events. J. Phys. Chem. B 109, p. 6688
15. C. Dellago, P. Bolhuis, F. S. Csajka, and D. Chandler (1998) Transition path sampling and the calculation of rate constants J. Chem. Phys. 108, pp. 1964-1977
16. C. Dellago, P. Bolhuis, and P. Geissler (2002) Transition path sampling. Adv. Chem. Phys. 123, pp. 1-78
17. A. K. Faradjian and R. Elber (2004) Computing time scales from reaction coordinates by milestoning. J. Chem Phys. 120, pp. 10880-10889
18. H. Grubmüller (1995) Predicting slow structural transitions in macromolecular systems: Conformational flooding. Phys. Rev. E 52, pp. 2893-2906
19. D. Cvijovic and J. Klinowski (1995) Taboo search - an approach to the multiple minima problem. Science 267, pp. 664-666
20. T. Huber, A. Torda, and W. van Gunsteren (1994) Local elevation: A method for improving the searching properties of molecular dynamics simulation. J. Comput. Aided Mol. Des. 8, pp. 695-708
21. A. K. N. Nakajima, J. Higo and H. Nakamura (1997) Flexible docking of a ligand peptide to a receptor protein by multicanonical molecular dynamics simulation. Chem. Phys. Lett. 278, pp. 297-301
22. B. A. Heymann and H. Grubmüller (2001) Molecular dynamics force probe simulations of antibody/antigen unbinding: Entropic control and nonadditivity of unbinding forces. Biophys. J. 81, pp. 1295-1313
23. H. G. and J. H. (2000) Improved tangent estimate in the nudged elastic band method for finding minimum energy paths and saddle points. J. Chem. Phys. 113, pp. 9978-9985
24. R. Fletcher and M. J. D. Powell (1963) A rapidly convergent descent method for minimization. Comput. J. 6, pp. 163-168
25. J. Gullingsrud, R. Braun, and K. Schulten (1999) Reconstructing potentials of mean force through time series analysis of steered molecular dynamics simulations. J. Comp. Phys. 151, pp. 190-211
26. R. Elber and M. Karplus (1987) A method for determining reaction paths in large molecules - application to myoglobin. Chem. Phys. Lett. 139, p. 375
27. A. Laio and M. Parrinello (2002) Escaping free energy minima. Proc. Natl. Acad. Sci. USA 99, pp. 12562-12566
28. C. Theodoropoulos, Y. Qian, and I. G. Kevrekidis (2000) Coarse stability and bifurcation analysis using time-steppers: A reaction-diffusion example. Proc. Natl. Acad. Sci. USA 97, pp. 9840-9843
29. I. G. Kevrekidis, C. W. Gear, and G. Hummer (2004) Equation-free: The computer-aided analysis of comptex multiscale systems. Aiche J. 50(7), pp. 1346-1355
30. C. Micheletti, A. Laio, and M. Parrinello (2004) Reconstructing the density of states by history-dependent metadynamics. Phys. Rev. Lett. 92, p. 170601
31. F. Wang and D. Landau (2001) Efficient, multiple-range random walk algorithm to calculate the density of states. Phys. Rev. Lett. 86, p. 2050
32. G. Bussi, A. Laio, and M. Parrinello (2006) Equilibrium free energies from nonequilibrium metadynamics. Phys. Rev. Lett. 96, p. 090601
33. R. Martoňák, A. Laio, and M. Parrinello (2003) Predicting crystal structures: The parrinello-rahman method revisited. Phys. Rev. Lett. 90, p. 75503
34. P. Raiteri, R. Martoňák, and M. Parrinello (2005) Exploring polymorphism: The case of benzene. Angew. Chem. Int. Ed. 44, pp. 3769-3773
35. R. Martoňacak, A. Laio, M. Bernasconi, C. Ceriani, P. Raiteri, and M. Parrinello (2005) Simulation of structural phase transitions by metadynamics. Zeitschrift fur Kristallographie 220, pp. 489-498
36. M. Iannuzzi, A. Laio, and M. Parrinello (2003) Efficient exploration of reactive potential energy surfaces using car-m. parrinelloolecular dynamics. Phys Rev. Lett. 90, p. 238302
37. A. Stirling, M. Iannuzzi, A. Laio, and M. Parrinello (2004) Azulene-tonaphthalene rearrangement: The car-parrinello metadynamics method explores various reaction mechanisms. Chem. Phys. Chem. 5, pp. 1558-156
38. S. Churakov, M. Iannuzzi, and M. Parrinello (2004) Ab initio study of dehydroxylation-carbonation reaction on brucite surface. J. Phys. Chem. B 108, p. 11567
39. F. Gervasio, A. Laio, M. Iannuzzi, and M. Parrinello (2004) Influence of dna structure on the reactivity of the guanine radical cation. Chem. Eur. J. 10, p. 4846
40. B. Ensing, A. Laio, F. Gervasio, M. Parrinello, and M. Klein (2004) A minimum free energy reaction path for the e2 reaction between fluoro ethane and a fluoride ion. J. Am. Chem. Soc. 126(31), p. 9492
41. B. Ensing and M. L. Klein (2005) Perspective on the reactions between f- and ch3ch2f: The free energy landscape of the e2 and s(n)2 reaction channels. Proc. Natl. Acad. Sci. USA 102, pp. 6755-6759
42. Y. Wu, J. Schmitt, and R. Car (2004) Mapping potential energy surfaces. J. Chem. Phys. 121, pp. 1193-1200
43. M. Ceccarelli, C. Danelon, A. Laio, and M. Parrinello (2004) Microscopic mechanism of antibiotics translocation through a porin. Biophys J. 87, pp. 58-64
44. F. L. Gervasio, A. Laio, and M. Parrinello (2005) Flexible docking in solution using metadynamics. J. Am. Chem. Soc. 127, pp. 2600-2607
45. D. Branduardi, F. L. Gervasio, A. Cavalli, M. Recantini, and M. Parrinello (2005) The role of the peripheral anionic site and cation-pi interactions in the ligand penetration of the human ache gorge. J. Am. Chem. Soc. 127(25), p. 9147
46. F. Zipoli, M. Bernasconi, and R. Martoňák (2004) Constant pressure reactive molecular dynamics simulations of phase transitions under pressure: The graphite to diamond conversion revisited. Eur. Phys. J. B 39, p. 41
47. M. Iannuzzi and M. Parrinello (2004) Proton transfer in heterocycle crystals. Phys. Rev. Lett. 93, p. 025901
48. D. Donadio, P. Raiteri, and M. Parrinello (2005) Topological defects and bulk melting of hexagonal ice. J. Phys. Chem. B 109, p. 5421
49. R. Car and M. Parrinello (1985) Unified approach for molecular-dynamics and density-functional theory. Phys. Rev. Lett. 45, p. 2471
50. M. Parrinello and A. Rahman (1980) Crystal structure and pair potentials: A molecular-dynamics study. Phys. Rev. Lett. 45, p. 1196
51. S. Nose (1984) A unified formulation of the constant temperature moleculardynamics methods. J. Chem. Phys. 81, pp. 511-519
52. H. C. Andersen (1980) Molecular-dynamics simulations at constant pressure and-or temperature. J. Chem. Phys. 72, pp. 2384-2393
53. B. Ensing, A. Laio, M. Parrinello, and M. Klein (2005) A recipe for the computation of the free energy barrier and the lowest free energy path of concerted reactions. J. Phys. Chem. B 109, pp. 6676-6687
54. R. Zwanzig (1961) Memory effects in irreversible thermodynamics. Phys. Rev. 124, pp. 983-992
55. H. Ottinger (1998) General projection operator formalism for the dynamics and thermodynamics of complex fluids. Phys. Rev. E 57, p. 1416
56. A. Laio, A. Rodriguez-Fortea, F. L. Gervasio, M. Ceccarelli, and M. Parrinello (2005) Assessing the accuracy of metadynamics. J. Phys. Chem. B 109, pp. 6714-6721
57. C. Gardiner (2004) Handbook of Stochastic Methods. Springer Berlin Heidelberg
58. M. Ceccarelli, F. Mercuri, D. Passerone, and M. Parrinello (2005) The microscopic switching mechanism of a [2]catenane. J. Phys. Chem. B 109, pp. 17094-17099
59. P. Raiteri, A. Laio, F. L. Gervasio, C. Micheletti, and M. Parrinello (2006) Efficient reconstruction of complex free energy landscapes by multiple walkers metadynamics. J. Phys. Chem. B 110, pp. 3533-3539