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Determination of free energy profiles by repository based adaptive umbrella sampling: Bridging nonequilibrium and quasiequilibrium simulations

J. Chem. Phys. 128, 204106 (2008); doi:10.1063/1.2920476

Published 27 May 2008

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Han Zheng and Yingkai Zhang
Department of Chemistry, New York University, New York, New York 10003, USA
We propose a new adaptive sampling approach to determine free energy profiles with molecular dynamics simulations, which is called as “repository based adaptive umbrella sampling” (RBAUS). Its main idea is that a sampling repository is continuously updated based on the latest simulation data, and the accumulated knowledge and sampling history are then employed to determine whether and how to update the biasing umbrella potential for subsequent simulations. In comparison with other adaptive methods, a unique and attractive feature of the RBAUS approach is that the frequency for updating the biasing potential depends on the sampling history and is adaptively determined on the fly, which makes it possible to smoothly bridge nonequilibrium and quasiequilibrium simulations. The RBAUS method is first tested by simulations on two simple systems: a double well model system with a variety of barriers and the dissociation of a NaCl molecule in water. Its efficiency and applicability are further illustrated in ab initio quantum mechanics/molecular mechanics molecular dynamics simulations of a methyl-transfer reaction in aqueous solution. ©2008 American Institute of Physics
History: Received 5 March 2008; accepted 16 April 2008; published 27 May 2008
Permalink: http://link.aip.org/link/?JCPSA6/128/204106/1
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KEYWORDS and PACS

Keywords
PACS
  • 82.60.Lf
    Thermodynamics of solutions (chemistry)
  • 82.20.Db
    Transition state theory and statistical theories of rate constants (chemical kinetics)
  • 82.30.Fi
    Ion-molecule, ion-ion, and charge-transfer chemical reactions
  • 82.30.Lp
    Decomposition chemical reactions (pyrolysis, dissociation, and fragmentation)
  • YEAR: 2008

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ISSN:
0021-9606 (print)   1089-7690 (online)
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REFERENCES (56)
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  1. C. Chipot and A. Pohorille, Free Energy Calculations: Theory and Applications in Chemistry and Biology (Springer, New York, 2007).
  2. J. G. Kirkwood, J. Chem. Phys. 3, 300 (1935).
  3. L. D. Landau and E. M. Lifshiz, Statistical Physics, 2nd ed. (Pergamon, New York, 1969), pp. 343–353.
  4. R. W. Zwanzig, J. Chem. Phys. 22, 1420 (1954).
  5. G. N. Patey and J. P. Valleau, J. Chem. Phys. 63, 2334 (1975).
  6. M. Mezei, J. Comput. Phys. 68, 237 (1987).
  7. C. Jarzynski, Phys. Rev. E 56, 5018 (1997).
  8. A. Laio and M. Parrinello, Proc. Natl. Acad. Sci. U.S.A. 99, 12562 (2002).
  9. W. E and E. Vanden-Eijnden, Lect. Notes Comput. Sci. Eng. Springer-Verlag, Berlin, 39, 35 (2004).
  10. L. Maragliano and E. Vanden-Eijnden, Chem. Phys. Lett. 446, 182 (2007).
  11. T. Lelievre, M. Rousset, and G. Stoltz, J. Chem. Phys. 126, 134111 (2007).
  12. S. Marsili, A. Barducci, R. Chelli, P. Procacci, and V. Schettino, J. Phys. Chem. B 110, 14011 (2006).
  13. G. Bussi, A. Laio, and M. Parrinello, Phys. Rev. Lett. 96, 090601 (2006).
  14. J. Kastner and W. Thiel, J. Chem. Phys. 123, 144104 (2005).
  15. E. Gallicchio, M. Andrec, A. K. Felts, and R. M. Levy, J. Phys. Chem. B 109, 6722 (2005).
  16. D. Hamelberg, J. Mongan, and J. A. Mccammon, J. Chem. Phys. 120, 11919 (2004).
  17. L. Rosso, P. Minary, Z. W. Zhu, and M. E. Tuckerman, J. Chem. Phys. 116, 4389 (2002).
  18. E. Darve, M. A. Wilson, and A. Pohorille, Mol. Simul. 28, 113 (2002).
  19. J. A. Rahman and J. C. Tully, J. Chem. Phys. 116, 8750 (2002).
  20. F. G. Wang and D. P. Landau, Phys. Rev. E 64, 056101 (2001).
  21. E. Darve and A. Pohorille, J. Chem. Phys. 115, 9169 (2001).
  22. J. R. Gullingsrud, R. Braun, and K. Schulten, J. Comput. Phys. 151, 190 (1999).
  23. Y. Sugita and Y. Okamoto, Chem. Phys. Lett. 314, 141 (1999).
  24. M. Sprik and G. Ciccotti, J. Chem. Phys. 109, 7737 (1998).
  25. C. Bartels and M. Karplus, J. Comput. Chem. 18, 1450 (1997).
  26. A. F. Voter, Phys. Rev. Lett. 78, 3908 (1997).
  27. H. Grubmuller, Phys. Rev. E 52, 2893 (1995).
  28. B. Roux, Comput. Phys. Commun. 91, 275 (1995).
  29. S. Kumar, D. Bouzida, R. H. Swendsen, P. A. Kollman, and J. M. Rosenberg, J. Comput. Chem. 13, 1011 (1992).
  30. C. Bartels, M. Schaefer, and M. Karplus, J. Chem. Phys. 111, 8048 (1999).
  31. R. Rajamani, K. J. Naidoo, and J. L. Gao, J. Comput. Chem. 24, 1775 (2003).
  32. J. Wang, Y. Gu, and H. Y. Liu, J. Chem. Phys. 125, 094907 (2006).
  33. F. Calvo, Mol. Phys. 100, 3421 (2002).
  34. J. Henin and C. Chipot, J. Chem. Phys. 121, 2904 (2004).
  35. B. Ensing, M. De Vivo, Z. W. Liu, P. Moore, and M. L. Klein, Acc. Chem. Res. 39, 73 (2006).
  36. T. Lelievre, M. Rousset, and G. Stoltz, J. Comput. Phys. 222, 624 (2007).
  37. H. Li, D. Min, Y. Liu, and W. Yang, J. Chem. Phys. 127, 094101 (2007).
  38. V. Babin, C. Roland, T. A. Darden, and C. Sagui, J. Chem. Phys. 125, 204909 (2006).
  39. S. Boresch and M. Karplus, J. Chem. Phys. 105, 5145 (1996).
  40. P. Raiteri, A. Laio, F. L. Gervasio, C. Micheletti, and M. Parrinello, J. Phys. Chem. B 110, 3533 (2006).
  41. J. W. Ponder, TINKER, Software Tools for Molecular Design, Version 4.2 (The most updated version for the TINKER program can be obtained from J. W. Ponder's world wide web site at http://dasher.wustl.edu/tinker., 2004).
  42. M. J. Frisch, G. W. Trucks, H. B. Schlegel et al., GAUSSIAN 03, Revision B.05 (Gaussian, Inc., Pittsburgh, PA, 2003).
  43. R. J. Renka, ACM Trans. Math. Softw. 19, 81 (1993).
  44. S. Koneshan and J. C. Rasaiah, J. Chem. Phys. 113, 8125 (2000).
  45. R. A. Friedman and M. Mezei, J. Chem. Phys. 102, 419 (1995).
  46. M. Berkowitz, O. A. Karim, J. A. Mccammon, and P. J. Rossky, Chem. Phys. Lett. 105, 577 (1984).
  47. D. J. Mclennan, Aust. J. Chem. 31, 1897 (1978).
  48. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, J. Chem. Phys. 79, 926 (1983).
  49. J. Aqvist, J. Phys. Chem. 94, 8021 (1990).
  50. W. D. Cornell, P. Cieplak, I. Bayly, I. R. Gould, K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, and P. A. Kollman, J. Am. Chem. Soc. 117, 5179 (1995).
  51. A. M. Ferrenberg and R. H. Swendsen, Phys. Rev. Lett. 61, 2635 (1988).
  52. J. Chandrasekhar, S. F. Smith, and W. L. Jorgensen, J. Am. Chem. Soc. 106, 3049 (1984).
  53. S. Wang, P. Hu, and Y. Zhang, J. Phys. Chem. B 111, 3758 (2007).
  54. P. Hu, S. Wang, and Y. Zhang, J. Am. Chem. Soc. 130, 3806 (2008).
  55. C. Eckart, Phys. Rev. 35, 1303 (1930).
  56. W. H. Miller, J. Am. Chem. Soc. 101, 6810 (1979).

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