Hamiltonian replica exchange molecular dynamics using soft-core interactions

Journal of Chemical Physics

Volumn 128, Issue 14, 2008, Pages

  Hritz, Jozef ^a   Oostenbrink, Chris ^a  

^a VU UNIVERSITY AMSTERDAM   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMOLECULES; COMPUTER SIMULATION; CONFORMATIONS; ENERGY BARRIERS; EXCHANGE INTERACTIONS; HAMILTONIANS; OPTIMIZATION; PROBLEM SOLVING; SAMPLING;

HAMILTONIAN REPLICA EXCHANGE MOLECULAR DYNAMICS (H-REMD); HIGH ENERGY BARRIERS; SOFT CORE INTERACTIONS; SOFT CORE POTENTIALS;

MOLECULAR DYNAMICS;

BIOPOLYMER;

ARTICLE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; ENERGY TRANSFER;

BIOPOLYMERS; COMPUTER SIMULATION; ENERGY TRANSFER; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR CONFORMATION;

EID: 42149182885     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2888998     Document Type: Article

References (37)

1. C. L. Brooks III, M. Karplus, and B. M. Pettitt, Advances in Chemical Physics (Wiley, New York, 1988), Vol. 71.
2. M. Leitgeb, C. Schroder, and S. Boresch, J. Chem. Phys. 122, 084109 (2005).
3. J. P. Valleau and S. G. Whittington, in Statistical Mechanics, edited by, B. J. Berne, (Plenum, New York, 1977), Chap., p. 145.
4. U. H. E. Hansmann, Chem. Phys. Lett. 281, 140 (1997).
5. H. Fukunishi, O. Watanabe, and S. Takada, J. Chem. Phys. 116, 9058 (2002).
6. Y. Sugita, A. Kitao, and Y. Okamoto, J. Chem. Phys. 113, 6042 (2000).
7. T. C. Beutler, A. E. Mark, R. C. van Schaik, P. R. Gerber, and W. F. van Gunsteren, Chem. Phys. Lett. 222, 529 (1994).
8. D. D. Frantz, D. L. Freeman, and J. D. Doll, J. Chem. Phys. 93, 2769 (1990).
9. H. Li, G. Li, B. A. Berg, and W. Yang, J. Chem. Phys. 125, 144902 (2006).
10. A. Okur, D. R. Roe, C. Guanglei, V. Hornak, and C. Simmerling, J. Chem. Theory Comput. 3, 557 (2007).
11. J. Hritz and C. Oostenbrink, J. Chem. Phys. 127, 204104 (2007).
12. R. Stolarski, C. E. Hagberg, and D. Shugar, Eur. J. Biochem. 138, 187 (1984).
13. W. F. van Gunsteren, S. R. Billeter, A. A. Eising, P. H. Hünenberger, P. Krüger, A. E. Mark, W. R. P. Scott, and I. G. Tironi, Biomolecular Simulation: The GROMOS96 Manual and User Guide (Vdf Hochschulverlag AG an der ETH Zürich, Zürich, 1996).
14. M. Christen, P. H. Hunenberger, D. Bakowies, R. Baron, R. Burgi, D. P. Geerke, T. N. Heinz, M. A. Kastenholz, V. Krautler, C. Oostenbrink, C. Peter, D. Trzesniak, and W. F. Van Gunsteren, J. Comput. Chem. 26, 1719 (2005).
15. R. H. Swendsen and J. S. Wang, Phys. Rev. Lett. 57, 2607 (1986).
16. Y. Sugita and Y. Okamoto, Chem. Phys. Lett. 314, 141 (1999).
17. M. Christen, A.-P. E. Kunz, and W. F. Van Gunsteren, J. Phys. Chem. B 110, 8488 (2006).
18. J. G. Kirkwood, J. Chem. Phys. 3, 300 (1935).
19. J.-P. Ryckaert, G. Ciccotti, and H. J. C. Berendsen, J. Comput. Phys. 23, 327 (1977).
20. R. W. Hockney, Methods Comput. Phys. 9, 136 (1970).
21. H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. DiNola, and J. R. Haak, J. Chem. Phys. 81, 3684 (1984).
22. H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, and J. Hermans, in Intermolecular Forces, edited by, B. Pullman, (Reidel, Dordrecht, 1981), p. 331.
23. I. G. Tironi, R. Sperb, P. E. Smith, and W. F. van Gunsteren, J. Chem. Phys. 102, 5451 (1995).
24. C. Oostenbrink, A. Villa, A. E. Mark, and W. F. van Gunsteren, J. Comput. Chem. 25, 1656 (2004).
25. See EPAPS Document No. E-JCPSA6-128-509811 for force-field parameters of GTP and 8-Br-GTP. For more information on EPAPS, see http://www.aip.org/ pubservs/epaps.html.
26. M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids (Clarendon, Oxford, 1987).
27. H. Rosemeyer, G. Toth, B. Golankiewicz, Z. Kazimierczuk, W. Bourgeois, U. Kretschmer, H. P. Muth, and F. Seela, J. Org. Chem. 55, 5784 (1990).
28. G. M. Torrie and J. P. Valleau, J. Comput. Phys. 23, 187 (1977).
29. J. W. Pitera and W. C. Swope, Proc. Natl. Acad. Sci. U.S.A. 100, 7587 (2003).
30. P. Liu, B. Kim, R. A. Friesner, and B. J. Berne, Proc. Natl. Acad. Sci. U.S.A. 102, 13749 (2005).
31. A. Kone and D. A. Kofke, J. Chem. Phys. 122, 206101 (2005).
32. T. Läppchen, A. F. Hartog, V. A. Pinas, G. J. Koomen, and T. den Blaauwen, Biochemistry 44, 7879 (2005).
33. F. Schwede, A. Christensen, S. Liaw, T. Hippe, R. Kopperud, B. Jastorff, and S. O. Doskeland, Biochemistry 39, 8803 (2000).
34. B. C. Bookser, M. C. Matelich, K. Ollis, and B. G. Ugarkar, J. Med. Chem. 48, 3389 (2005).
35. B. C. Oostenbrink, J. W. Pitera, M. M. H. Van Lipzig, J. H. N. Meerman, and W. F. van Gunsteren, J. Med. Chem. 43, 4594 (2000).
36. C. Oostenbrink and W. F. van Gunsteren, Proteins 54, 237 (2004).
37. X. Cheng, G. Cui, V. Hornak, and C. Simmerling, J. Phys. Chem. B 109, 8220 (2005).