Preserving the Boltzmann ensemble in replica-exchange molecular dynamics

Journal of Chemical Physics

Volumn 129, Issue 16, 2008, Pages

  Cooke, Ben ^a   Schmidler, Scott C ^b  

^a DUKE UNIVERSITY   (United States)

^b Department of Statistical Science   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MOLECULAR DYNAMICS; OSCILLATORS (ELECTRONIC); QUANTUM CHEMISTRY;

ALANINE DIPEPTIDE; BOLTZMANN; CONFIGURATION SPACES; CONVERGENCE BEHAVIORS; DETERMINISTIC ALGORITHMS; EQUILIBRIUM CONFIGURATIONS; ERGODIC; HARMONIC OSCILLATORS; INITIAL CONFIGURATIONS; MINIMUM ENERGY CONFIGURATIONS; MIXTURE OF GAUSSIANS; MONTE CARLO; NUMERICAL INTEGRATORS; OKAMOTO; PHASE PLOTS; SIMPLE MODIFICATIONS; SMALL SYSTEMS; TEMPERATURE SIMULATIONS;

DYNAMICS;

ALANINE; DIPEPTIDE;

ALGORITHM; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; MONTE CARLO METHOD; PROBABILITY; PROTEIN CONFORMATION; TEMPERATURE; THERMODYNAMICS;

ALANINE; ALGORITHMS; DIPEPTIDES; MARKOV CHAINS; MODELS, MOLECULAR; MONTE CARLO METHOD; PROTEIN CONFORMATION; TEMPERATURE; THERMODYNAMICS;

EID: 55349094650     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2989802     Document Type: Article

References (51)

1. Y. Sugita and Y. Okamoto, Chem. Phys. Lett. 314, 141 (1999).
2. C. J. Geyer, Markov chain Monte Carlo maximum likelihood, in Computing Science and Statistics: Proceedings of the 23rd Symposium on Interface, 1991, pp. 156-163.
3. P. H. Nguyen, Y. Mu, and G. Stock, Proteins: Struct., Funct., Genet. 60, 485 (2005).
4. M. M. Seibert, A. Patriksson, B. Hess, and D. van der Spoel, J. Mol. Biol. 354, 173 (2005).
5. W. Zhang, C. Wu, and Y. Duan, J. Chem. Phys. 123, 154105 (2005).
6. B. Cooke and S. C. Schmidler, " Statistical prediction and molecular dynamics simulation.," Biophys. J. (in press).
7. D. A. Beck, G. W. White, and V. Daggett, J. Struct. Biol. 157, 514 (2007).
8. X. Periole and A. E. Mark, J. Chem. Phys. 126, 014903 (2007).
9. A. E. Roitberg, A. Okur, and C. Simmerling, J. Phys. Chem. B 111, 2415 (2007).
10. N. Madras and Z. Zheng, Random Struct. Algorithms 1, 66 (2003).
11. D. Woodard, S. C. Schmidler, and M. Huber, " Conditions for rapid mixing of parallel and simulated tempering on multimodal distributions.," Ann. Appl. Probab. (to be published).
12. N. Bhatnagar and D. Randall, " Torpid mixing of simulated tempering on the Potts model.," in Proceedings of the 15th ACM/SIAM Symposium on Discrete Algorithms (SODA), 2004, pp. 478-487.
13. D. Woodard, S. C. Schmidler, and M. Huber, " Sufficient conditions for torpid mixing of parallel and simulated tempering on multimodal distributions.," Electron. J. Probab. (submitted).
14. M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids (Oxford University Press, New York, 1987).
15. D. J. Evans and G. P. Morriss, Statistical Mechanics of Non-Equilibrium Liquids (Academic, New York, 1990).
16. D. Frenkel and B. Smit, Understanding Molecular Simulation (Academic, New York, 1996).
17. A. R. Leach, Molecular Modelling: Principles and Applications (Addison Wesley Longman, New York, 1996).
18. P. Billingsley, Probability and Measure, 3rd ed. (Wiley, New York, 1995).
19. G. H. Choe, Computational Ergodic Theory (Springer-Verlag, Berlin, 2005).
20. N. Metropolis, A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller, and E. Teller, J. Chem. Phys. 21, 1087 (1953).
21. V. I. Arnold, Mathematical Methods of Classical Mechanics 2nd ed. (Springer-Verlag, Berlin, 1989).
22. P. J. Channell and C. Scovel, Nonlinearity 3, 231 (1990).
23. H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsterenand, A. DiNola, and J. R. Haak, J. Chem. Phys. 81, 3684 (1984).
24. X. Daura, B. Juan, D. Seebach, W. F. van Gunsteren, and A. E. Mark, J. Mol. Biol. 280, 925 (1998).
25. X. Daura, K. Gademann, B. Jaun, D. Seebach, and W. F. van Gunsteren, Angew. Chem., Int. Ed. 38, 236 (1999).
26. A. E. Garcia and K. Y. Sanbonmatsu, Proc. Natl. Acad. Sci. U.S.A. 99, 2782 (2002).
27. L. J. Smith, X. Daura, and W. F. van Gunsteren, Proteins: Struct., Funct., Genet. 48, 487 (2002).
28. H. Nymeyer and A. E. Garcia, Proc. Natl. Acad. Sci. U.S.A. 100, 13934 (2003).
29. D. A. Pearlman, Comput. Phys. Commun. 91, 1 (1995).
30. J. C. Phillips, J. Comput. Chem. 26, 1781 (2005).
31. E. Lindahl, B. Hess, and D. van der Spoel, J. Mol. Model. 7, 306 (2001).
32. T. Morishita, J. Chem. Phys. 113, 2976 (2000).
33. S. Noś, J. Chem. Phys. 81, 511 (1984).
34. W. G. Hoover, Phys. Rev. A 31, 1695 (1985).
35. R. G. Winkler, V. Kraus, and P. Reineker, J. Chem. Phys. 102, 9018 (1995).
36. G. J. Martyna, M. L. Klein, and M. Tuckerman, J. Chem. Phys. 97, 2635 (1992).
37. S. D. Bond, B. J. Leimkuhler, and B. B. Laird, J. Comput. Phys. 151, 114 (1999).
38. S. Noś, J. Phys. Soc. Jpn. 70, 75 (2001).
39. B. B. Laird and B. J. Leimkuhler, Phys. Rev. E 68, 016704 (2003).
40. B. J. Leimkuhler and C. R. Sweet, J. Chem. Phys. 121, 108 (2004).
41. S. Duane, A. D. Kennedy, B. J. Pendleton, and D. Roweth, Phys. Lett. B 195, 216 (1987).
42. R. W. Pastor, in The Molecular Dynamics of Liquid Crystals, edited by, G. R. Luckhurst, and, C. A. Veracini, (Kluwer Academic, Dordrecht, 1994), pp. 85-138.
43. W. K. Hastings, Biometrika 57, 97 (1970).
44. R. M. Neal, " Probabilistic inference using Markov chain Monte Carlo methods.," Technical Report No. CRG-TR-93-1, University of Toronto, 1993.
45. J. S. Liu, Monte Carlo Strategies in Scientific Computing (Springer-Verlag, Berlin, 2001).
46. S. P. Meyn and R. L. Tweedie, Markov Chains and Stochastic Stability (Springer-Verlag, Berlin, 1993).
47. A. Brünger, C. Brooks III, and M. Karplus, Chem. Phys. Lett. 105, 495 (1984).
48. J. Mattingly, A. M. Stuart, and D. J. Higham, Stochastic Proc. Appl. 101, 185 (2002).
49. G. O. Roberts and R. L. Tweedie, Bernoulli 2, 341 (1996).
50. G. O. Roberts and J. S. Rosenthal " Examples of adaptive MCMC.," J. Comp. Graph. Stat. (unpublished).
51. S. Toxvaerd, Phys. Rev. E 47, 343 (1993).