Optimal reduced dimensional representation of classical molecular dynamics

Journal of Chemical Physics

Volumn 119, Issue 11, 2003, Pages 5379-5387

  Dey, Bijoy K ^a   Rabitz, H ^a   Askar, Attila ^b  

^a PRINCETON UNIVERSITY   (United States)

^b KOÇ UNIVERSITY   (Turkey)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; DEGREES OF FREEDOM (MECHANICS); ELECTRON ENERGY LEVELS; GENETIC ALGORITHMS; RELAXATION PROCESSES;

SUBSPACE METHODS;

MOLECULAR DYNAMICS;

EID: 0142087541     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.1599349     Document Type: Article

References (40)

1. C. L. Brooks, M. Karplus, and B. M. Pettitt, Proteins: A Theoretical Perspective of Dynamics, Structure and Thermodynamics (Wiley-Interscience, New York, 1988).
2. M. Karplus, Modeling of Molecular Structures and Properties, edited by J. L. Rivail (Elsevier Science, Amsterdam, 1990), p. 427
3. Y. X. Chang and K. F. Freed, J. Chem. Phys. 99, 8016 (1993).
4. A. M. Nyberg and T. Schlick, Chem. Phys. Lett. 198, 538 (1992).
5. B. R. Brooks, D. Janezic, and M. Karplus, J. Comput. Chem. 16, 1522 (1995).
6. D. A. Case, Curr. Opin. Struct. Biol. 4, 285 (1994).
7. C. Schutte, A. Fischer, W. Huisinga, and P. Deuflhard, J. Comput. Phys. 151, 146 (1999).
8. T. Ichiye and M. Karplus, Proteins 11, 205 (1991).
9. A. Kitao, F. Hirata, and N. Go, Chem. Phys. 158, 447 (1991).
10. A. E. Garcia, Phys. Rev. Lett. 68, 2696 (1992).
11. L. Sirovich and J. D. Rodriguez, Phys. Lett. A 120, 211 (1987).
12. D. H. Lu and W. L. Hase, J. Chem. Phys. 89, 6723 (1988).
13. A. Kuppermann, J. Phys. Chem. 83, 171 (1979).
14. Q. Sun and J. M. Bowman, J. Chem. Phys. 92, 1021 (1990).
15. J. M. Bowman, Adv. Chem. Phys. 61, 115 (1985).
16. Q. Sun and J. M. Bowman, Int. J. Quantum Chem. Quantum Chem. Symp. 23, 115 (1989).
17. J. P. Ryckaert, G. Ciccotti, and H. J. C. Berendsen, J. Comput. Phys. 23, 327 (1977).
18. S. Miyamoto and P. A. Kollman, J. Comput. Chem. 13, 952 (1992).
19. D. J. Tobias and C. L. Brooks, J. Chem. Phys. 89, 5115 (1988).
20. S. G. Lambrakos and M. Peyrard, J. Chem. Phys. 93, 4329 (1990).
21. Y. Qin and D. L. Thompson, J. Chem. Phys. 96, 1992 (1992).
22. A. Amadei, A. B. M. Linssen, and H. J. C. Berendsen, Proteins 17, 412 (1993).
23. T. Horiuchi and N. Go, Proteins 10, 106 (1991).
24. D. M. F. Van Aalten, A. Amadei, A. B. M. Linssen, V. G. H. Eijsink, G. Vriend, and H. J. C. Berendsen, Proteins 22, 45 (1995).
25. M. A. Balsera, W. Wriggers, Y. Oono, and K. Schulten, J. Phys. Chem. 100, 2567 (1996).
26. S. C. Phillips, J. W. Essex, and C. M. Edge, J. Chem, Phys. 112, 2586 (2000).
27. R. B. Sessions, P. D. Osguthorpe, and D. J. Osguthorpe, J. Mol. Biol. 210, 617 (1989).
28. P. D. Osguthorpe, C. M. Maunder, and D. J. Osguthorpe, J. Comput.-Aided Mol. Des. 10, 177 (1996).
29. M. Levitt, J. Mol. Biol. 220, 1 (1991).
30. A. Askar, A. E. Cetin, and H. Rabitz, J. Phys. Chem. 100, 19165 (1996).
31. H. Lu, B. Isralewitz, A. Krammer, V. Vogel, and K. Schulten, Biophys. J. 75, 662 (1998).
32. C. Schutte and F. A. Bornemann, Nonlinear Analysis-Theory, Method Applications 30, 1805 (1997).
33. B. Space, H. Rabitz, and A. Askar, J. Chem. Phys. 99, 9070 (1993).
34. A. Askar, B. Space, and H. Rabitz, J. Phys. Chem. 99, 7330 (1995).
35. K. Willcox and J. Peraire, AIAA J. 40, 2323 (2002).
36. K. Willcox, J. Paduano, J. Peraire, and K. Hall, AIAA Paper 99-1467, Proceedings of 40th AIAA Structures, Structural Dynamics and Materials Conference, 1999.
37. S. R. Ladd, Genetic Algorithms in C++ (M and T Books, New York, 1996); D. E. Goldberg, Genetic Algorithms in Search, Optimization arid Machine Learning (Addison-Wesley, New York, 1989).
38. S. R. Ladd, Genetic Algorithms in C++ (M and T Books, New York, 1996); D. E. Goldberg, Genetic Algorithms in Search, Optimization arid Machine Learning (Addison-Wesley, New York, 1989).
39. N. Go and H. A. Scheraga, Macromolecules 9, 535 (1976).
40. B. K. Dey, H. Rabitz, and A. Askar (unpublished).