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A hybrid recursion method to robustly ensure convergence efficiencies in the simulated scaling based free energy simulations

J. Chem. Phys. 129, 034105 (2008); doi:10.1063/1.2953321

Published 18 July 2008

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Lianqing Zheng,1 Irina O. Carbone,1 Alexey Lugovskoy,2 Bernd A. Berg,3 and Wei Yang1,4,5
1Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
2Molecular Modeling, Drug Discovery Department, Biogen IDEC Inc., 14 Cambridge Center, Cambridge, Massachusetts 02142, USA
3Department of Physics, Florida State University, Tallahassee, Florida 32306, USA
4Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
5College of Life Science, Nankai University, Tianjin 300071, P. R. China
Recently, we developed an efficient free energy simulation technique, the simulated scaling (SS) method [H. Li et al., J. Chem. Phys. 126, 024106 (2007)], in the framework of generalized ensemble simulations. In the SS simulations, random walks in the scaling parameter space are realized so that both phase space overlap sampling and conformational space sampling can be simultaneously enhanced. To flatten the distribution in the scaling parameter space, in the original SS implementation, the Wang–Landau recursion was employed due to its well-known recursion capability. In the Wang–Landau recursion based SS free energy simulation scheme, at the early stage, recursion efficiencies are high and free energy regions are quickly located, although at this stage, the errors of estimated free energy values are large; at the later stage, the errors of estimated free energy values become smaller, however, recursions become increasingly slow and free energy refinements require very long simulation time. In order to robustly resolve this efficiency problem during free energy refinements, a hybrid recursion strategy is presented in this paper. Specifically, we let the Wang–Landau update method take care of the early stage recursion: the location of target free energy regions, and let the adaptive reweighting method take care of the late stage recursion: the refinements of free energy values. As comparably studied in the model systems, among three possible recursion procedures, the adaptive reweighting recursion approach is the least favorable one because of its low recursion efficiency during free energy region locations; and compared to the original Wang–Landau recursion approach, the proposed hybrid recursion technique can be more robust to guarantee free energy simulation efficiencies. ©2008 American Institute of Physics
History: Received 18 February 2008; accepted 11 June 2008; published 18 July 2008
Permalink: http://link.aip.org/link/?JCPSA6/129/034105/1
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KEYWORDS and PACS

Keywords
PACS
  • 05.70.Ce
    Thermodynamic functions and equations of state
  • 71.15.-m
    Methods of electronic structure calculations (condensed matter)
  • YEAR: 2008

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0021-9606 (print)   1089-7690 (online)
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REFERENCES (24)
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  1. D. L. Beveridge and F. M. Dicapua, Annu. Rev. Biophys. Biophys. Chem. 18, 431 (1989);
  2. P. Kollman, Chem. Rev. (Washington, D.C.) 93, 2395 (1993);
  3. J. M. Rickman and R. LeSar, Annu. Rev. Mater. Res. 32, 195 (2002);
  4. T. Simonson, G. Archontis, and M. Karplus, Acc. Chem. Res. 35, 430 (2002);
  5. D. Lu and T. Woolf, in Free Energy Calculations: Theory and Applications in Chemistry and Biology, Springer Series in Chemical Physics, edited by A. Pohorille and C. Chipot (Springer, New York, 2007), Vol. 86;
  6. S. A. Adcock and J. A. McCammon, Chem. Rev. (Washington, D.C.) 106, 1589 (2006);
  7. M. R. Shirts, D. L. Mobley, and J. D. Chodera, Annu. Rep. Comp. Chem. 3, 41 (2007);
  8. W. Yang, H. Nymeyer, H. X. Zhou, B. A. Berg, and R. Brüschweiler, J. Comput. Chem. 29, 668 (2008).
  9. D. Min, H. Li, G. Li, R. Bitetti-Putzer, and W. Yang, J. Chem. Phys. 126, 144109 (2007).
  10. H. Li and W. Yang, J. Chem. Phys. 126, 114104 (2007).
  11. H. Li, M. Fajer, and W. Yang, J. Chem. Phys. 126, 024106 (2007).
  12. A. P. Lyubartsev, A. A. Martinovski, S. V. Shevkunov, and P. N. Vorontsov-Velyaminov, J. Chem. Phys. 96, 1776 (1992);
    13. E. Marinari and G. Parisi, Europhys. Lett. 19, 451 (1992);
    A. Irbäck and F. Potthast, J. Chem. Phys. 103, 10298 (1995);
    U. H. E. Hansmann and Y. Okamoto, Phys. Rev. E 54, 5863 (1996);
    U. H. E. Hansmann and Y. Okamoto, J. Comput. Chem. 18, 920 (1997);
    E. Marinari, G. Parisi, and J. J. Ruiz-Lorenzo, in Spin Glasses and Random Fields, edited by A. P. Young (World Scientific, Singapore, 1998), pp. 59–98;
    A. Irbäck and E. Sandelin, J. Chem. Phys. 110, 12256 (1999).
  13. M. I. Fajer, H. Li, W. Yang, and P. G. Fajer, J. Am. Chem. Soc. 129, 13840 (2007).
  14. S. Boresch and M. Karplus, J. Phys. Chem. A 103, 103 (1999);
    15. 103, 119 (1999).
  15. M. Zaharias, T. P. Straatsma, and J. A. McCammon, J. Chem. Phys. 100, 9025 (1994).
  16. B. L. Tembe and J. A. McCammon, Comp. Chem. 8, 281 (1984);
    17. T. P. Straatsma and J. A. McCammon, Annu. Rev. Phys. Chem. 43, 407 (1992).
  17. F. Wang and D. P. Landau, Phys. Rev. Lett. 86, 2050 (2001);
    18. 64, 056101 (2001).
  18. C. Bartels and M. Karplus, J. Comput. Chem. 18, 1450 (1997).
  19. B. A. Berg and T. Celik, Phys. Rev. Lett. 69, 2292 (1992);
    20. B. A. Berg, J. Stat. Phys. 82, 323 (1996).
  20. B. A. Berg, Comput. Phys. Commun. 153, 397 (2003).
  21. S. Duane, A. D. Kennedy, and B. J. Pendleton, and D. Roweth, Phys. Lett. B 195, 216 (1987).
  22. P. Dayal, S. Trebst, S. Wessel, D. Würtz, M. Troyer, S. Sabhapandit, and S. N. Coppersmith, Phys. Rev. Lett. 92, 097201 (2004);
    23. D. P. Landau, S.-H. Tsai, and M. Exler, Am. J. Phys. 72, 1294 (2004);
    A. Malakis, S. S. Martinos, I. A. Hadjiagapiou, and A. S. Peratzakis, Int. J. Mod. Phys. C 15, 729 (2004);
    C. Zhou and R. N. Bhatt, Phys. Rev. E 72, 025701 (2005);
    D. Earl and M. Deem, J. Phys. Chem. B 109, 6701 (2005);
    H. K. Lee, Y. Okabe, and D. P. Landau, Comput. Phys. Commun. 175, 36 (2006);
    R. E. Belardinelli and V. D. Pereyra, Phys. Rev. E 75, 046701 (2007);
    J. Chem. Phys. 127, 184105 (2007).
  23. G. M. Torrie and J. P. Valleau, J. Comput. Phys. 23, 187 (1977).
  24. A. M. Ferrenberg and R. H. Swendsen, Phys. Rev. Lett. 63, 1195 (1989).
  25. M. Karpusas, J. Lucci, J. Ferrant, C. Benjamin, F. R. Taylor, K. Strauch, E. Garber, and Y. M. Hsu, Structure (London) 9, 321 (2001).
  26. A. D. Mackerell, Jr., D. Bashford, M. Bellot et al., J. Phys. Chem. B 102, 3586 (1998).
  27. W. Im, S. Berneche, and B. Roux, J. Chem. Phys. 114, 2924 (2001).
  28. L. Zheng and W. Yang, J. Chem. Phys. (unpublished).
  29. B. A. Berg, Markov Chain Monte Carlo Simulations and Their Statistical Analysis (World Scientific, Singapore, 2004), p. 85.
  30. M. R. Shirts and V. S. Pande, J. Chem. Phys. 122, 144107 (2005);
    31. F. M. Ytreberg, ibid. 125, 184114 (2006).
  31. D. Min, Y. Liu, I. Carbone, and W. Yang, J. Chem. Phys. 126, 194104 (2007).

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