Extending molecular dynamics time scales with milestoning: Example of complex kinetics in a solvated peptide

Journal of Chemical Physics

Volumn 126, Issue 14, 2007, Pages

  West, Anthony M A ^a   Elber, Ron ^b   Shalloway, David ^c  

^a Cornell University   (United States)

^b Department of Computer Science and School of Operations Research and Information Engineering   (United States)

^c Department of Obstetrics Gynecology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BLOCKED ALANINE; CONFORMATIONAL TRANSITION; NON-MARKOVIAN MODELS; NONEXPONENTIAL;

ALGORITHMS; COMPUTER SIMULATION; CONFORMATIONS; COORDINATION REACTIONS; DIFFUSION; PEPTIDES;

MOLECULAR DYNAMICS;

PEPTIDE; SOLVENT;

ALGORITHM; ARTICLE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; KINETICS; PHASE TRANSITION; PROTEIN CONFORMATION;

ALGORITHMS; COMPUTER SIMULATION; KINETICS; MODELS, CHEMICAL; MODELS, MOLECULAR; PEPTIDES; PHASE TRANSITION; PROTEIN CONFORMATION; SOLVENTS;

EID: 34247210226     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2716389     Document Type: Article

References (37)

1. New Algorithms for Macromolecular Simulation, edited by B. Leimkuhler, C. Chipot, R. Elber, A. Laaksonen, A. Mark, T. Schlick, C. Scutle, and R. Skeek (Springer, Berlin, 2006).
2. G. Jayachandran, V. Vishal, and V. S. Pande, J. Chem. Phys. 124, 164092 (2006).
3. A. K. Faradjian and R. Elber, J. Chem. Phys. 120, 10880 (2004).
4. D. Shalloway and A. K. Faradjian, J. Chem. Phys. 124, 054112 (2006).
5. D. G. Truhlar, B. C. Garrett, and S. J. Klippenstein, J. Phys. Chem. 100, 12771 (1996).
6. H. Eyring, J. Chem. Phys. 3, 107 (1935).
7. B. Ensing, M. De Vivo, Z. W. Liu, P. Moore, and M. L. Klein, Acc. Chem. Res. 39, 73 (2006).
8. R. Elber, A. Roitberg, C. Simmerling, R. Goldstein, H. Y. Li, G. Verkhivker, C. Keasar, J. Zhang, and A. Ulitsky, Comput. Phys. Commun. 91, 159 (1995).
9. A. Ulitsky and R. Elber, J. Chem. Phys. 92, 1510 (1990).
10. H. Jonsson, G. Mills, and K. W. Jacobsen, in Classical and Quantum Dynamics in Condensed Phase Simulations, edited by B. J. Berne, G. Ciccotti, and D. F. Coker (World Scientific, Singapore, 1998), p. 385.
11. E. Weinan, R. Weiqing, and E. Vanden-Eijnden, Phys. Rev. B 66, 52301 (2002).
12. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, J. Chem. Phys. 79, 926 (1983).
13. J. P. Ryckaert, G. Ciccotti, and H. J. C. Berendsen, J. Comput. Phys. 23, 327 (1977).
14. W. L. Jorgensen and J. Tirado-Rives, J. Am. Chem. Soc. 110, 1666(1988).
15. T. A. Darden, A. Toukmaji, and L. G. Pedersen, J. Chim. Phys. Phys.-Chim. Biol. 94, 1346 (1997).
16. R. Elber, J. Chem. Phys. 93, 4312 (1990).
17. D. Moroni, P. R. ten Wolde, and P. G. Bolhuis, Phys. Rev. E 71, 056709 (2005).
18. P. Haenggi and P. Talkner, Phys. Rev. Lett. 51, 2242 (1983).
19. S. J. Weiner, P. A. Kollman, D. A. Case, U. C. Singh, C. Ghio, G. Alagona, S. Profeta, and P. Weiner, J. Am. Chem. Soc. 106, 765 (1984).
20. B. L. de Groot and H. Grubmuller, Science 294, 2353 (2001).
21. Y. Duan and P. A. Kollman, Science 282, 740 (1998).
22. V. S. Pande, I. Baker, J. Chapman et al., Biopolymers 68, 91 (2003).
23. A. F. Voter, F. Montalenti, and T. C. Germann, Annu. Rev. Mater. Res. 32, 321 (2002).
24. C. Dellago, P. G. Bolhuis, and P. L. Geissler, Adv. Chem. Phys. 123, 1 (2002).
25. A. Ma and A. Dinner, J. Phys. Chem. B 109, 6769 (2005).
26. H. Jonsson, G. Mills, and K. W. Jacobsen, in Classical and Quantum Dynamics in Condensed Phase Simulations, edited by B. J. Berne, G. Ciccotti, and D. F. Coker (World Scientific, Singapore, 1998), p. 385.
27. W. Ren, E. Vanden-Eijnden, and P. Maragakis, J. Chem. Phys. 123, 134109 (2005).
28. R. Elber, A. Ghosh, and A. Cardenas, Ace. Chem. Res. 35, 396 (2002).
29. E. Weinan, W. Ren, and E. Vanden-Eijnden, Chem. Phys. Lett. 413, 242 (2005).
30. T. S. van Erp, D. Moroni, and P. G. Bolhuis, J. Chem. Phys. 118, 7762 (2003).
31. G. Hummer and I. G. Kevrekidis, J. Chem. Phys. 118, 10762 (2003).
32. G. A. Huber and S. Kim, Biophys. J. 70, 97 (1996).
33. D. Moroni, P. G. Bolhuis, and T. S. van Erp, J. Chem. Phys. 120, 4055 (2004).
34. A. B. Kolomeisky and M. E. Fisher, J. Chem. Phys. 113, 10867 (2000).
35. J. Straub, D. Hsu, and B. Berne, J. Phys. Chem. 89, 5188 (1985).
36. R. Elber, Biophys. J. (accepted).
37. G. Arfken, Mathematical Methods for Physicists (Academic, San Diego, 1985).