Molecular dynamics simulations of a fully hydrated dipalmitoylphosphatidylcholine bilayer with different macroscopic boundary conditions and parameters

Journal of Chemical Physics

Volumn 105, Issue 11, 1996, Pages 4871-4880

  Tieleman, D P ^a   Berendsen, H J C ^a  

^a UNIVERSITY OF GRONINGEN   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0000112789     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.472323     Document Type: Article

References (60)

1. R. Pastor and R. Venable, in Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications, edited by W. van Gunsteren, P. Weiner, and A. Wilkinson (Escom Science, Leiden, 1993), Chap. 2, pp. 443-464.
2. Membrane Structure and Dynamics, edited by K. Merz and B. Roux (to be published).
3. P. van der Ploeg and H. J. C. Berendsen, J. Chem. Phys. 76, 3271 (1982), It should be noted that there is a significant typographic error in the paper. For both methylene and methyl σ should be σ=0.374 nm.
4. P. van der Ploeg and H. Berendsen, Mol. Phys. 49, 243 (1982).
5. E. Egberts, Ph.D. thesis, University of Groningen, The Netherlands, 1988.
6. E. Egberts and H. Berendsen, J. Chem. Phys. 89, 3718 (1988).
7. J. López Cascales, J. García de la Torre, S. Marrink, and H. Berendsen, J. Chem. Phys. 104, 2713 (1996).
8. E. Egberts, S. Marrink, and H. Berendsen, Eur. Biophys. J. 22, 423 (1993).
9. E. Jakobsson and H. Scott, in Ref. 2.
10. S.-W. Chiu et al., Biophys. J. 69, 1500 (1995).
11. S. E. Feller, Y. Zhang, and R. W. Pastor, J. Chem. Phys. 103, 10267 (1995).
12. Y. Zhang, S. E. Feller, B. R. Brooks, and R. W. Pastor, J. Chem. Phys. 103, 10252 (1995).
13. W. F. van Gunsteren and H. J. C. Berendsen, GROMOS-87 Manual, (Biomos BV, Nijenborgh 4, 9747 AG Groningen, The Netherlands, 1987).
14. A. R. van Buuren, S. J. Marrink, and H. J. C. Berendsen, J. Phys. Chem. 97, 9206 (1993).
15. S. J. Marrink and H. J. C. Berendsen, J. Phys. Chem. 98, 4155 (1994).
16. S. J. Marrink, F. Jähnig, and H. J. C. Berendsen, Biophys. J. (in press).
17. H. J. C. Berendsen, J. P. M. Postma, W. F. Gunsteren, and J. Hermans, Intermolecular Forces, edited by B. Pullman (Reidel, Dordrecht, 1981).
18. H. Berendsen, J. Grigera, and T. Straatsma, J. Phys. Chem. 91, 6269 (1987).
19. W. L. Jorgensen, J. Am. Chem. Soc. 103, 335 (1981).
20. Y. Guissani and B. Guillot, J. Chem. Phys. 98, 8221 (1993).
21. J. Hermans, A. Pathiaseril, and A. Anderson, J. Am. Chem. Soc. 110, 5982 (1988).
22. S. Marrink, M. Berkowitz, and H. Berendsen, Langmuir 9, 3122 (1993).
23. R. W. Hockney and J. W. Eastwood, Computer Simulations Using Particles (McGraw-Hill, New York, 1981).
24. B. A. Luty, I. G. Tironi, and W. F. van Gunsteren, J. Chem. Phys. 103, 3014 (1995).
25. T. Darden, D. York, and L. Pedersen, J. Chem. Phys. 98, 10089 (1993).
26. H. Berendsen, D. van der Spoel, and R. van Drunen, Comp. Phys. Comm. 91, 43 (1995).
27. H. Heller, M. Schaefer, and K. Schulten, J. Phys. Chem. 97, 8343 (1993).
28. P. Smith and W. van Gunsteren, in Computer Simulation of Biomolecular Systems, edited by W. van Gunsteren, P. Weiner, and A. Wilkinson (ESCOM Science, Leiden, The Netherlands, 1993), Vol. 2, pp. 182-212.
29. H. Alper, D. Bassolino, and T. Stouch, J. Chem. Phys. 98, 9798 (1993).
30. S. Chiu, K. Gulukota, and E. Jakobsson, in Membrane Proteins: Structures, Interactions and Models, edited by A. Pullman, J. Jortner, and B. Pullman (Kluwer, Dordrecht, 1992), pp. 315-338.
31. P. Huang, J. Perez, and G. Loew, J. Biomol. Struct. Dynam. 11, 927 (1994).
32. R. Venable, Y. Zhang, B. Hardy, and R. Pastor, Science 262, 223 (1993).
33. K. Damodaran and K. Merz, Biophys. J. 66, 1076 (1994).
34. A. Robinson, W. Richards, P. Thomas, and M. Hann, Biophys. J. 67, 2345 (1994).
35. H. Berendsen, J. Postma, W. van Gunsteren, A. DiNola, and J. Haak, J. Chem. Phys. 81, 3684 (1984).
36. T. McIntosh, Biochemistry 25, 4058 (1986).
37. F. Jähnig, Biophys. J. 46, 687 (1984).
38. J. Nagle, Annu. Rev. Phys. Chem. 31, 157 (1980).
39. F. Jähnig, Biophys. J. (in press).
40. T. L. Hill, Introduction to Statistical Mechanics (Dover, Mineola, NY, 1986).
41. M. J. Ruocco and G. G. Shipley, Biochim. Biophys. Acta 691, 309 (1982).
42. Y. Inoko and T. Mitsui, J. Phys. Soc. Jpn. 44, 1918 (1978).
43. M. J. Janiak, D. M. Small, and G. G. Shipley, Biochemistry 15, 4575 (1976).
44. J. P. Ryckaert, G. Ciccotti, and H. J. C. Berendsen, J. Comput. Phys. 23, 327 (1977).
45. L. Lis, M. McAlister, N. Fuller, and R. Rand, Biophys. J. 37, 657 (1982).
46. B. Lewis and D. Engleman, J. Mol. Biol. 166, 211 (1983).
47. H. Schindler and J. Seelig, Biochemistry 14, 2283 (1975).
48. R. Pace and S. Chan, J. Chem. Phys. 76, 4217 (1982).
49. L. De Young and K. Dill, Biochemistry 27, 5281 (1988).
50. R. Thurmond, S. Dodd, and M. Brown, Biophys. J. 59, 108 (1991).
51. J. Nagle, Biophys. J. 64, 1476 (1993).
52. R. Rand and V. Parsegian, Biochim. Biophys. Acta 988, 351 (1989).
53. S. Church, D. Griffiths, R. Lewis, R. McElhaney, and H. Wickman, Biophys. J. 49, 597 (1986).
54. K. Gawrisch et al., Biophys. J. 61, 1213 (1992).
55. J. Nagle and M. Wiener, Biochim. Biophys. Acta 942, 1 (1988).
56. M. Wiener and S. White, Biophys. J. 61, 434 (1992).
57. R. Flewelling and W. Hubbell, Biophys. J. 49, 541 (1986).
58. S. Simon and T. McIntosh, Proc. Natl. Acad. Sci. USA 86, 9263 (1989).
59. J. Seelig, Q. Rev. Biophys. 10, 353 (1977).
60. J. Seelig and A. Seelig, Q. Rev. Biophys. 13, 19 (1980).