Molecular dynamics simulation of polymer helix formation using rigid-link methods

Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics

Volumn 66, Issue 1, 2002, Pages

  Rapaport, D C ^a  

^a BAR ILAN UNIVERSITY   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; DENSITY (SPECIFIC GRAVITY); DIFFUSION; HYDROGEN BONDS; ISOTHERMS; MATHEMATICAL MODELS; MOLECULAR DYNAMICS; MOLECULAR STRUCTURE; SILICA; THERMODYNAMICS;

DENSITY DEPENDENCE; LIQUID SILICA; MOLECULAR STRUCTURAL ORDER; SIMPLE POINT CHARGE MODEL (SPC/E);

MOLECULAR PHYSICS;

EID: 41349104240     PISSN: 1063651X     EISSN: None     Source Type: Journal    
DOI: 10.1103/PhysRevE.66.011906     Document Type: Article

References (33)

1. C. L. Brooks III, M. Karplus, and B. M. Pettit, Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics (Wiley, New York, 1988).
2. K. A. Dill, S. Bromberg, K. Yue, K. M. Fiebig, D. P. Yee, P. D. Thomas, and H. S. Chan, Protein Sci. 4, 561 (1995).
3. E. I. Shakhnovich, Curr. Opin. Struct. Biol. 7, 29 (1997).
4. C. L. Brooks III, Curr. Opin. Struct. Biol. 8, 222 (1998).
5. V. S. Pande, A. Y. Grosberg, and T. Tanaka, Rev. Mod. Phys. 72, 259 (2000).
6. Y. Duan and P. A. Kollman, Science 282, 740 (1998).
7. H. J. C. Berendsen, Science 282, 642 (1998).
8. M. Levitt and A. Warshel, Nature (London) 253, 694 (1975).
9. G. M. Crippen and Y. Z. Ohkubo, Proteins 32, 425 (1998).
10. H. Goldstein, Classical Mechanics, 2nd ed. (Addison-Wesley, Reading, MA, 1980).
11. J.-P. Ryckaert, G. Ciccotti, and H. J. C. Berendsen, J. Comput. Phys. 23, 327 (1977).
12. G. Ciccotti, M. Ferrario, and J.-P. Ryckaert, Mol. Phys. 47, 1253 (1982).
13. H. C. Anderson, J. Comput. Phys. 52, 24 (1983).
14. R. Edberg, D. J. Evans, and G. P. Morriss, J. Comput. Phys. 84, 6933 (1986).
15. D. C. Rapaport, The Art of Molecular Dynamics Simulation (Cambridge University Press, Cambridge, 1995).
16. G. Rodriguez and K. Kreutz-Delgado, IEEE Trans. Rob. Autom. 8, 65 (1992).
17. A. Jain, J. Guid. Control Dyn. 14, 531 (1991).
18. R. A. Bertsch, N. Vaidehi, S. L. Chan, and W. A. Goddard III, Proteins 33, 343 (1998).
19. A. Dullweber, B. Leimkuhler, and R. McLachlan, J. Comput. Phys. 107, 5840 (1997).
20. A. Jain, N. Vaidehi, and G. Rodriguez, J. Comput. Phys. 106, 258 (1993).
21. K. S. Fu, R. C. Gonzalez, and C. C. G. Lee, Robotics: Control, Sensing, Vision, and Intelligence (McGraw-Hill, New York, 1987).
22. A. Jain and G. Rodriguez, IEEE Trans. Rob. Autom. 11, 585 (1995).
23. W. H. Press, S. A. Teukolsky, W. T. Vetterling, and B. R. Flannery, Numerical Recipes in C: The Art of Scientific Computing, 2nd ed. (Cambridge University Press, Cambridge, 1992).
24. L. Verlet, Phys. Rev. 159, 98 (1967).
25. D. J. Evans, Mol. Phys. 34, 317 (1977).
26. D. C. Rapaport and H. A. Scheraga, Macromolecules 14, 1238 (1981).
27. B. L. de Groot, X. Daura, A. E. Mark, and H. Grubmüller, J. Mol. Biol. 309, 299 (2001).
28. J. C. Nelson, J. G. Saven, J. S. Moore, and P. G. Wolynes, Science 277, 1793 (1997).
29. Y. Ueda, H. Taketomi, and N. Go, Biopolymers 17, 1531 (1978).
30. E. M. Boczko and C. L. Brooks III, Science 269, 393 (1995).
31. Y. Zhou and M. Karplus, Nature (London) 401, 400 (1999).
32. Y. Zhou, M. Karplus, J. M. Wichert, and C. K. Hall, J. Chem. Phys. 107, 10691 (1997).
33. K. Huang, Statistical Mechanics (Wiley, New York, 1963).