Molecular dynamics with the united-residue model of polypeptide chains. I. Lagrange equations of motion and tests of numerical stability in the microcanonical mode

Journal of Physical Chemistry B

Volumn 109, Issue 28, 2005, Pages 13785-13797

  Khalili, Mey ^a   Liwo, Adam ^a,b   Rakowski, Franciszek ^c,d   Grochowski, Paweł ^c   Scheraga, Harold A ^a  

^a Department of Obstetrics Gynecology   (United States)

^b UNIVERSITY OF GDA SK   (Poland)

^c UNIVERSITY OF WARSAW   (Poland)

^d WARSAW UNIVERSITY OF TECHNOLOGY   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

ENERGY DRIFT; PHYSICS-BASED UNITED-RESIDUE (UNRES) FORCE FIELD; VELOCITY VERLET ALGORITHM; VIRTUAL BOND VECTORS;

ALGORITHMS; CHEMICAL BONDS; DEGREES OF FREEDOM (MECHANICS); EQUATIONS OF MOTION; POLYPEPTIDES; STEREOCHEMISTRY;

MOLECULAR DYNAMICS;

ALANINE; PEPTIDE; PROTEIN;

ALGORITHM; ARTICLE; CHEMICAL MODEL; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; KINETICS; METHODOLOGY; MOTION; PHYSICAL CHEMISTRY; PROTEIN DATABASE; STATISTICAL MODEL; THEORETICAL MODEL; THERMODYNAMICS; TIME;

ALANINE; ALGORITHMS; CHEMISTRY, PHYSICAL; COMPUTER SIMULATION; DATABASES, PROTEIN; KINETICS; MODELS, CHEMICAL; MODELS, STATISTICAL; MODELS, THEORETICAL; MOLECULAR CONFORMATION; MOTION; PEPTIDES; PROTEINS; THERMODYNAMICS; TIME FACTORS;

EID: 23144450194     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp058008o     Document Type: Article

References (72)

1. van Gunsteren, W. F. Molecular dynamics and stochastic dynamics: A primer. In Computer Simulation of Biomolecular Systems; van Gunsteren, W. F., Weiner, P. K., Wilkinson, A. J., Eds.; ESCOM: Leiden, The Netherlands, 1993; pp 3-36.
2. Fersht, A. R.; Daggett, V. Cell 2002, 108, 573.
3. Day, R.; Daggett, V. Adv. Protein Chem. 2003, 66, 373.
4. Shea, J.-E.; Brooks, C. L., III Annu. Rev. Phys. Chem. 2001, 52, 499.
5. Kubelka, J.; Hofrichter, J.; Eaton, W. A. Curr. Opin. Struct. Biol. 2004, 14, 76.
6. Elber, R.; Ghosh, A.; Cárdenas, A. Acc. Chem. Res. 2002, 35, 396.
7. Ghosh, A.; Elber, R.; Scheraga, H. A. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 10394.
8. Duan, Y.; Kollman, P. A. Science 1998, 282, 740.
9. Pande, V. S.; Baker, I.; Chapman, J.; Elmer, S. P.; Khaliq, S.; Larson, S. M.; Rhee, Y. M.; Shirts, M. R.; Snow, C. D.; Sorin, E. J.; Zagrovic, B. Biopolymers 2003, 68, 91.
10. Jang, S.; Kim, E.; Shin, S.; Pak, Y. J. Am. Chem. Soc. 2003, 125, 14841.
11. Pearlman, D. A.; Case, D. A.; Caldwell, J. W.; Ross, W. S.; Cheatham, T. E., III.; DeBolt, S.; Ferguson, D.; Seibel, G.; Kollman, P. Comput. Phys. Commun. 1995, 91, 1.
12. Case, D. A.; Pearlman, D. A.; Caldwell, J. W.; Cheatham, T. E., III; Wang, J.; Ross, W. S.; Simmerling, C. L.; Darden, T. A.; Merz, K. M.; Stanton, R. V.; Cheng, A. L.; Vincent, J. J.; Crowley, M.; Tsui, V.; Gohlke, H.; Radmer, R. J.; Duan, Y.; Pitera, J.; Massova, I.; Siebel, G. L.; Singh, U. C.; Weiner, P. K.; Kollman, P. A. AMBER 7; University of California: San Francisco, CA, 2002.
13. Cramer, C. J.; Truhlar, D. G. Chem. Rev. 1999, 99, 2161.
14. Bashford, D.; Case, D. A. Annu. Rev. Phys. Chem. 2000, 51, 129.
15. Veitshans, T.; Klimov, D.; Thirumalai, D. Folding Des. 1996, 2, 1.
16. Klimov, D. K.; Thirumalai, D. Phys. Rev. Lett. 1997, 79, 317.
17. He, S.; Scheraga, H. A. J. Chem. Phys. 1998, 108, 271.
18. He, S.; Scheraga, H. A. J. Chem. Phys. 1998, 108, 287.
19. Hoang, T. X.; Cieplak, M. J. Chem. Phys. 2000, 112, 6851.
20. Cieplak, M.; Hoang, T. X.; Robbins, M. O. Proteins: Struct., Funct., Genet. 2002, 49, 104.
21. Sorenson, J. M.; Head-Gordon, T. Proteins: Struct., Funct., Genet. 2002, 46, 368.
22. Koretke, K. K.; Luthey-Schulten, Z.; Wolynes, P. G. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 2932.
23. Hardin, C.; Eastwood, M. P.; Luthey-Schulten, Z.; Wolynes, P. G. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 14235.
24. Takada, S. Proteins: Struct., Funct., Genet. 2001, 42, 85.
25. Hardin, C.; Eastwood, M. P.; Prentiss, M.; Luthey-Schulten, Z.; Wolynes, P. G. J. Comput. Chem. 2002, 23, 138.
26. Hardin, C.; Eastwood, M. P.; Prentiss, M. C.; Luthey-Schulten, Z.; Wolynes, P. G. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 1679.
27. Fujitsuka, Y.; Takada, S.; Luthey-Schulten, Z. A.; Wolynes, P. G. Proteins: Struct., Funct., Genet. 2004, 54, 88.
28. Kolinski, A.; Godzik, A.; Skolnick, J. J. Chem. Phys. 1993, 98, 7420.
29. Kolinski, A.; Skolnick, J. Proteins: Struct., Funct., Genet. 1994, 18, 338.
30. Kolinski, A.; Skolnick, J. Proteins: Struct., Funct., Genet. 1994, 18, 353.
31. Kolinski, A.; Rotkiewicz, P.; Ilkowski, B.; Skolnick, J. Prog. Theor. Phys. Suppl. 2000, 138, 292.
32. Rudnicki, W. R.; Bakalarski, G.; Lesyng, B. J. Biomol. Struct. Dyn. 2000, 17, 1097.
33. Kilmister, C. W. Lagrangian Dynamics: An Introduction for Students; Logos Press Limited: London, U. K., 1967.
34. Maciejczyk, M.; Rudnicki, W. R.; Lesyng, B. J. Biomol. Struct. Dyn. 2000, 17, 1109.
35. Liwo, A.; Pincus, M. R.; Wawak, R. J.; Rackovsky, S.; Scheraga, H. A. Protein Sci. 1993, 2, 1715.
36. Liwo, A.; Ołdziej, S.; Pincus, M. R.; Wawak, R. J.; Rackovsky, S.; Scheraga, H. A. J. Comput. Chem. 1997, 18, 849.
37. Liwo, A.; Pincus, M. R.; Wawak, R. J.; Rackovsky, S.; Ołdziej, S.; Scheraga, H. A. J. Comput. Chem. 1997, 18, 874.
38. Liwo, A.; Kaźnierkiewicz, R.; Czaplewski, C.; Groth, M.; Ołdziej, S.; Wawak, R. J.; Rackovsky, S.; Pincus, M. R.; Scheraga, H. A. J. Comput. Chem. 1998, 19, 259.
39. Liwo, A.; Lee, J.; Ripoll, D. R.; Pillardy, J.; Scheraga, H. A. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 5482.
40. Liwo, A.; Czaplewski, C.; Pillardy, J.; Scheraga, H. A. J. Chem. Phys. 2001, 115, 2323.
41. Lee, J.; Ripoll, D. R.; Czaplewski, C.; Pillardy, J.; Wedemeyer, W. J.; Scheraga, H. A. J. Phys. Chem. B 2001, 105, 7291.
42. Pillardy, J.; Czaplewski, C.; Liwo, A.; Wedemeyer, W. J.; Lee, J.; Ripoll, D. R.; Arłukowicz, P.; Ołdziej, S.; Arnautova, Y. A.; Scheraga, H. A. J. Phys. Chem. B 2001, 105, 7299.
43. Pillardy, J.; Czaplewski, C.; Liwo, A.; Lee, J.; Ripoll, D. R.; Kaźmierkiewicz, R.; Ołdziej, S.; Wedemeyer, W. J.; Gibson, K. D.; Arnautova, Y. A.; Saunders, J.; Ye, Y.-J.; Scheraga, H. A. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 2329.
44. Liwo, A.; Arłukowicz, P.; Czaplewski, C.; Ołdziej, S.; Pillardy, J.; Scheraga, H. A. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 1937.
45. Ołdziej, S.; Kozłowska, U.; Liwo, A.; Scheraga, H. A. J. Phys. Chem. A 2003, 107, 8035.
46. Liwo, A.; Ołdziej, S.; Czaplewski, C.; Kozłowska, U.; Scheraga, H. A. J. Phys. Chem. B 2004, 108, 9421.
47. Liwo, A.; Arłukowicz, P.; Ołdziej, S.; Czaplewski, C.; Makowski, M.; Scheraga, H. A. J. Phys. Chem. B 2004, 108, 16918.
48. Ołdziej, S.; Liwo, A.; Czaplewski, C.; Pillardy, J.; Scheraga, H. A. J. Phys. Chem. B 2004, 108, 16934.
49. Ołdziej, S.; Ła̧giewka, J.; Liwo, A.; Czaplewski, C.; Chinchio, M.; Nanias, M.; Scheraga, H. A. J. Phys. Chem. B 2004, 108, 16950.
50. Lee, J.; Scheraga, H. A.; Rackovsky, S. J. Comput. Chem. 1997, 18, 1222.
51. Lee, J.; Liwo, A.; Scheraga, H. A. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 2025.
52. Lee, J.; Liwo, A.; Ripoll, D. R.; Pillardy, J.; Scheraga, H. A. Proteins Struct., Funct., Genet. 1999, Suppl. 3, 204.
53. Ołdziej, S.; Czaplewski, C.; Liwo, A.; Chinchio, M.; Nanias, M.; Vila, J. A.; Khalili, M.; Arnautova, Y. A.; Jagielska, A.; Makowski, M.; Schafroth, H. D.; Kaźmierkiewicz, R.; Ripoll, D. R.; Pillardy, J.; Saunders, J. A.; Kang, Y.-K.; Gibson, K. D.; Scheraga, H. A. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 7547.
54. Khalili, M.; Liwo, A.; Jagielska, A.; Scheraga, H. A. J. Phys. Chem. B 2005, 109, 13798.
55. Liwo, A.; Khalili, M.; Scheraga, H. A. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 2362.
56. van Kampen, C. W. Phys. Rep. 1985, 124, 69.
57. Sprik, M.; Ciccotti, G. J. Chem. Phys. 1998, 109, 7737.
58. Verlet, L. Phys. Rev. 1967, 159, 98.
59. Hockney, R. W.; Eastwood, J. W. Computer Simulations Using Particles; McGraw-Hill: New York, 1981.
60. Beeman, D. J. Comput. Phys. 1976, 20, 130.
61. Swope, W. C.; Andersen, H. C.; Berens, P. H.; Wilson, K. R. J. Chem. Phys. 1982, 76, 637.
62. Ruth, R. IEEE Trans. Nucl. Sci. 1983, 30, 2669.
63. Calvo, M. P.; Sanz-Serna, J. M. Numerical Hamiltonian Problems; Chapman & Hall: London, U. K., 1994.
64. Benettin, G.; Giorgilli, A. J. Stat. Phys. 1994, 74, 1117.
65. Tuekerman, M.; Berne, B. J.; Martyna, G. J. J. Chem. Phys. 1992, 97, 1990.
66. Ciccotti, G.; Kalibaeva, G. Philos. Trans. R. Soc. London, Ser. A 2004, 362, 1583.
67. Martyna, G. J.; Tuckerman, M. E.; Tobias, D. J.; Klein, M. L. Mol. Phys. 1996, 87, 1117.
68. Stocker, U.; Juchli, D.; van Gunsteren, W. F. Mol. Simul. 2003, 29, 123.
69. Litniewski, M. Mol. Simul. 2003, 29, 223.
70. Czaplewski, C.; Liwo, A.; Pillardy, J.; Ołziej, S.; Scheraga, H. A. Polymer 2004, 45, 677.
71. Gibson, K. D.; Scheraga, H. A. J. Comput. Chem. 1990, 11, 468.
72. Thompson, P. A.; Muñoz, V.; Jas, G. S.; Henri, E. R.; Eaton, W. A.; Hofrichter, J. J. Phys. Chem. B 2000, 104, 378.