A skewed-momenta method to efficiently generate conformational-transition trajectories

Journal of Chemical Physics

Volumn 123, Issue 7, 2005, Pages

  MacFadyen, James ^a   Andricioaei, Ioan ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

JARZYNSKI IDENTITY; KINETIC PROPERTIES; PUDDLE JUMPING; REWEIGHTING SCHEME; SKEWED-MOMENTA METHOD; TRANSITION TRAJECTORIES;

COMPUTATIONAL METHODS; FREE ENERGY; ISOMERIZATION; MAXWELL EQUATIONS; METHOD OF MOMENTS; TRAJECTORIES;

CONFORMATIONS;

ARTICLE; CHEMICAL MODEL; COMPUTER SIMULATION; CONFORMATION; ENTROPY; KINETICS; METHODOLOGY; PHYSICAL CHEMISTRY; STATISTICAL MODEL; TEMPERATURE; THEORETICAL MODEL; THERMODYNAMICS; TIME;

CHEMISTRY, PHYSICAL; COMPUTER SIMULATION; ENTROPY; KINETICS; MODELS, CHEMICAL; MODELS, STATISTICAL; MODELS, THEORETICAL; MOLECULAR CONFORMATION; TEMPERATURE; THERMODYNAMICS; TIME FACTORS;

EID: 34547139165     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2000242     Document Type: Article

References (43)

1. C. Dellago, P. G. Bolhuis, F. S. Csajka, and D. Chandler, J. Chem. Phys. 108, 1964 (1998).
2. C. Dellago, P. G. Bolhuis, and D. Chandler, J. Chem. Phys. 110, 6617 (1999).
3. G. Hummer and A. Szabo, Proc. Natl. Acad. Sci. U.S.A. 98, 3659 (2001).
4. D. Chandler, Introduction to Modern Statistical Mechanics (Oxford University Press, New York, 1987).
5. C. Jarzynski, Phys. Rev. Lett. 78, 2690 (1997).
6. D. J. Bicout and A. Szabo, Protein Sci. 9, 452 (2000).
7. This is akin to the "golf course" problem often cited in minimization literature pertinent to protein folding (Ref. 43) having to do with finding a deep hole on a large, flat (i. e., enthalpically barrierless) surface.
8. H. Oberhofer, C. Dellago, and P. L. Geissler, J. Phys. Chem. B 109, 6902 (2005).
9. J. A. Rahman and J. C. Tully, Chem. Phys. 285, 277 (2002).
10. S. A. Corcelli, J. A. Rahman, and J. C. Tully, J. Chem. Phys. 118, 1085 (2003).
11. A. F. Voter, Phys. Rev. Lett. 78, 3908 (1997).
12. A. F. Voter, J. Chem. Phys. 106, 4665 (1997).
13. D. Hamelberg, J. Mongan, and J. A. McCammon, J. Chem. Phys. 120, 11919 (2004).
14. A. Laio and M. Parrinello, Proc. Natl. Acad. Sci. U.S.A. 99, 12562 (2002).
15. G. A. Huber and S. Kim, Biophys. J. 70, 97 (1996).
16. H. Grubmuller, Phys. Rev. E 52, 2893 (1995).
17. E. Carter, G. Ciccotti, J. Haynes, and R. Kapral, Chem. Phys. Lett. 156, 472 (1989).
18. M. Mella, J. Chem. Phys. 122, 204106 (2005).
19. K. Duffin and W. Barnett, Proceedings of the IEEE Conference on Scientific Visualization, Washington, DC, 1994 (IEEE Computer Society Press, Los Alamitos, CA, 1994), pp. 205-211.
20. A. Aguilera and R. Pérez-Aguila, in Short Communication Papers - Proceedings of the 12th International Conference on Computer Graphics, Visualization and Computer Vision, University of West Bohemia, Plzen, Czech. Republic, 2-6 Feb. (Union Agency-Science, 2004), pp. 1-8.
21. A. Amadei, A. Linssen, and H. Berendsen, Proteins 17, 412 (1993).
22. M. Balsera, W. Wriggers, Y. Oono, and K. Schulten, J. Phys. Chem. 100, 2567 (1996).
23. I. Andricioaei, A. R. Dinner, and M. Karplus, J. Chem. Phys. 118, 1074 (2003).
24. B. R. Brooks, D. Janezic, and M. Karplus, J. Comput. Chem. 16, 1522 (1995).
25. N. Go, T. Noguti, and T. Nishikawa, Proc. Natl. Acad. Sci. U.S.A. 80, 3696 (1983).
26. M. Levitt, C. Sander, and P. S. Stern, J. Mol. Biol. 181, 423 (1985).
27. B. Brooks and M. Karplus, Proc. Natl. Acad. Sci. U.S.A. 82, 4995 (1985).
28. J. P. Ma and M. Karplus, J. Mol. Biol. 274, 114 (1997).
29. Q. Cui, G. H. Li, J. P. Ma, and M. Karplus, J. Mol. Biol. 340, 345 (2004).
30. F. Tama and Y. H. Sanejouand, Protein Eng. 14, 1 (2001).
31. W. G. Krebs, V. Alexandrov, C. A. Wilson, N. Echols, H. Y. Yu, and M. Gerstein, Proteins 48, 682 (2002).
32. M. Delarue and Y. H. Sanejouand, J. Mol. Biol. 320, 1011 (2002).
33. F. Tama, M. Valle, J. Frank, and C. L. Brooks, Proc. Natl. Acad. Sci. U.S.A. 100, 9319 (2003).
34. O. Braun, A. Hanke, and U. Seifert, Phys. Rev. Lett. 93, 158105 (2004).
35. S. X. Sun, J. Chem. Phys. 118, 5769 (2003).
36. S. Mukamel, Phys. Rev. Lett. 90, 170604 (2003).
37. R. C. Lua and A. Y. Grosberg, J. Phys. Chem. B 109, 6805 (2005).
38. A. G. Palmer, Chem. Rev. (Washington, D.C.) 104, 3623 (2004).
39. H. Kleinert, Path Integrals in Quantum Mechanics, Statistics, Polymer Physics and Financial Markets, 3rd ed. (World Scientific, Singapore 2004).
40. L. Onsager and S. Machlup, Phys. Rev. 91, 1505 (1953).
41. R. Elber, J. Meller, and R. Olender, J. Phys. Chem. B 103, 899 (1999).
42. D. M. Zuckerman and T. B. Woolf, Phys. Rev. E 63, 016702 (2001).
43. J. D. Bryngelson and P. G. Wolynes, J. Phys. Chem. 93, 6902 (1989).