Molecular dynamics simulations of a polyalanine octapeptide under ewald boundary conditions: influence of artificial periodicity on peptide conformation

Journal of Physical Chemistry B

Volumn 104, Issue 15, 2000, Pages 3668-3675

  Weber, Wolfgang ^a   Hünenberger, Philippe H ^a,b   Andrew McCammon, J ^b,c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b ETH ZURICH   (Switzerland)

^c San Diego   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

APPROXIMATION THEORY; BOUNDARY CONDITIONS; COMPUTER SIMULATION; MOLECULAR DYNAMICS;

ARTIFICIAL PERIODICITY; EWALD BOUNDARY CONDITIONS; PEPTIDE CONFORMATION; POLYALANINE OCTAPEPTIDES;

DNA;

EID: 0343005873     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp9937757     Document Type: Article

References (55)

1. Harvey, S. C. Proteins: Struct. Fund. Genet. 1989, 5, 78.
2. Davis, M.E.; McCammon, J.A. Client. Rev. 1990, 90, 509.
3. Smith, P.E. In Computer simulation of biomolecular systems, theoretical and experimental applications; van Gunsteren, W. F., Weiner, P. K., Wilkinson, A. J., Eds.; ESCOM: Leiden, The Netherlands, 1993; Vol. II, pp 182-212.
4. Levy, R. M.; Gallicchio, E. Annu. Rev. Phys. Chem. 1998, 49, 531.
5. Sagui, C.; Darden, T. A. Annu. Rev. Biophys. Biomol. Struct. 1999, 28, 155.
6. Hünenberger, P. H. In Simulation and theory of electrostatic interactions in solution: Computational chemistry, biophysics, and aqueous solutions; Pratt, L. R., Hummer, G., Eds.; American Institute of Physics: New York, 1999; pp 17-83.
7. Ewald, P. P. Ann. Phys. 1921, 64, 253.
8. Hockney, R. W.; Eastwood, J. W. Computer simulation using particles; Institute of Physics Publishing: Bristol, 1988.
9. Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98, 10089.
10. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. J. Chem. Phys. 1995, 103, 8577.
11. Smith, P. E.; Pettitt, B. M. J. Chem. Phys. 1991, 95, 8430.
12. Schreiber, H.; Steinhauser, O. Biochemistry 1992, 31, 5856.
13. Schreiber, H.; Steinhauser, O. Chem. Phys. 1992, 168, 75.
14. York, D. M.; Darden, T. A.; Pedersen, L. G. J. Chem. Phys. 1993, 99, 8345.
15. Fox, T.; Kollman, P. A. Proteins: Struct. Fund. Genet. 1996, 25, 315.
16. Mohan, V.; Smith, P. E.; Pettitt, B. M. J. Phys. Chem. 1993, 97, 12984.
17. Cheatham III, T. E.; Kollman, P. A. J. Mol. Biol. 1996, 259, 434.
18. Young, M. A.; Ravishanker, G.; Beveridge, D. L. Biophys. J. 1997, 73, 2313.
19. Auffinger, P.; Westhof, E. Curr. Opin. Struct. Biol. 1998, 8, 227.
20. Neumann, M. Mol. Phys. 1983, 50, 841.
21. Neumann, M.; Steinhauser, O.; Pawley, G. S. Mol. Phys. 1984, 52, 97.
22. Wood, R. H. J. Chem. Phys. 1995, 103, 6177.
23. Brooks III, C. L.; Pettitt, B. M.; Karplus, M. J. Chem. Phys. 1985, 83, 5897.
24. Baker, N. A.; Hünenberger, P. H.; McCammon, J. A. J. Chem. Phys. 1999, 110, 10679.
25. Brooks III, C. L. J. Chem. Phys. 1987, 86, 5156.
26. Madura, J. D.; Pettitt, B. M. Chem. Phys. Lett. 1988, 150, 105.
27. Straatsma, T. P.; Berendsen, H. J. C. J. Chem. Phys. 1989, 89, 5876.
28. Pettitt, B.M.; Rossky, P. J. J. Chem. Phys. 1986, 84, 5836.
29. Dang, L. X.; Pettitt, B. M. J. Phys. Chem. 1990, 94, 4303.
30. Guardia, E.; Rey, R.; Padro, J. A. J. Chem. Phys. 1991, 95, 2823.
31. Dang, L. X.; Pettitt, B. M.; Rossky, P. J. J. Chem. Phys. 1992, 96, 4046.
32. Hummer, G.; Soumpasis, D. M.; Neumann, M. Mol. Phys. 1993, 81, 1155.
33. Bader, J. S.; Chandler, D. J. Phys. Chem. 1992, 96, 6423.
34. Schreiber, H.; Steinhauser, O. J. Mol. Biol. 1992, 228, 909.
35. Figueirido, F.; Del Buono, G. S.; Levy, R. M. J. Chem. Phys. 1995, 103, 6133.
36. Hummer, G.; Pratt, L. R.; Garcia, A. E. J. Phys. Chem. 1996, 100, 1206.
37. Figueirido, F.; Del Buono, G. S.; Levy, R. M. J. Phys. Chem. B 1997, 101, 5622.
38. Hummer, G.; Pratt, L. R.; Garcia, A. E. J. Chem. Phys. 1997, 107, 9275.
39. Hummer, G.; Pratt, L. R.; Garcia, A. E. J. Phys. Chem. A 1998, 102, 7885.
40. Sakane, S.; Ashbaugh, H. S.; Wood, R. H. J. Phys. Chem. B 1998, 102, 5673.
41. Hiinenberger, P. H.; McCammon, J. A. /. Chem. Phys. 1999, 110, 1856.
42. Hunenberger, P. H.; McCammon, J. A. Biophys. Chem. 1999, 78, 69.
43. Smith, P. E.; Pettitt, B. M. /. Chem. Phys. 1996, 105, 4289.
44. Smith, P. E.; Blatt, H. D.; Pettitt, B. M. J. Phys. Chem. B 1997, 101, 3886.
45. Luty, B. A.; van Gunsteren, W. F. J. Phys. Chem. 1996, 100, 2581.
46. Norberto de Souza, O.; Ornstein, R. L. Biophys. J. 1997, 72, 2395.
47. de Bakker, P. I. W.; Hunenberger, P. H.; McCammon, J. A. J. Mol. Biol. 1999, 285, 1811.
48. van Gunsteren, W. F.; Billeter, S. R.; Eising, A. A.; Hünenberger, P. H.; Krüger, P.; Mark, A; E.; Scott, W. R. P.; Tironi, I. G. Biomolecular simulation: The GROMOS96 manual and user guide; Verlag der Fachvereine: Zürich, 1996.
49. Daura, X.; Mark, A. E.; van Gunsteren, W. F. J. Comput. Chem. 1998, 19, 535.
50. Scott, W. R. P.; Hünenberger, P. H.; Tironi, I. G.; Mark, A. E.; Billeter, S. R.; Fennen, J.; Torda, A. E.; Huber, T.; Krüger, T.; van Gunsteren, W. F. J. Phys. Chem. A 1999, 103, 3596.
51. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Hermans, J. In Intennolecular Forces; Pullman, B., Ed., Reidel: Dordrecht, 1981; pp 331-342.
52. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684.
53. Ryckaert, J.-P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 327.
54. Madura, J. D.; Davis, M. E.; Gilson, M. K.; Wade, R. C.; Luty, B. A.; McCammon, J. A. In Reviews in computational chemistry; Lipkowitz, K. B., Boyd, D. B., Eds.; VCH Publishers, Inc.: New York, 1994; pp 229-267.
55. Chakrabartty, A.; Baldwin, R. L. Adv. Protein Chem. 1995, 46, 141.