Assessment of all-atom potentials for modeling membranes: Molecular dynamics simulations of solid and liquid alkanes and crystals of phospholipid fragments

Journal de Chimie Physique et de Physico-Chimie Biologique

Volumn 94, Issue 7-8, 1997, Pages 1482-1502

  Tobias, D J ^a,b   Tu, K ^a   Klein, M L ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

^b NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY   (United States)

Author keywords

Energy functions; Membranes; Molecular dynamics

Indexed keywords

ALKANE; PHOSPHOLIPID;

CALCULATION; COMPUTER SIMULATION; CONFERENCE PAPER; CRYSTAL STRUCTURE; ELECTRIC POTENTIAL; LIPID BILAYER; MEMBRANE STRUCTURE; MOLECULAR DYNAMICS; TECHNIQUE; X RAY DIFFRACTION;

EID: 0030813468     PISSN: 00217689     EISSN: None     Source Type: Journal    
DOI: 10.1051/jcp/1997941482     Document Type: Conference Paper

References (46)

1. Small, DM (1986) The physical chemistry of lipids 4. Plenum Press, New York.
2. Ryckaert, JP, McDonald, IR, Klein, ML (1989) Mol Phys 67, 957.
3. Pastor, RW (1994) Curr Opin Struct Biol 4, 486.
4. Tobias, DJ, Tu, K, Klein ML (1997) Curr Opin Coll Int Sci 2, 15.
5. Smith, GD, Yoon, DY (1994) J Chem Phys 100, 649.
6. Bareman, JP, Klein, ML (1992) In Interface dynamics and growth. Eds. Liang, KS, Anderson, MP, Bruinsma, RF, Scoles, G. Materials Research Society Proceedings, vol. 237, MRS, Pittsburgh.
7. Bareman, JP, Klein, ML (1987) J Phys Chem 94, 5202.
8. Hautman, J, Bareman, JP, Mar, W, Klein, ML (1991) J Chem Soc Faraday Trans 87, 2031.
9. Mar, W, Klein, ML (1994) Langmuir 10, 188.
10. Tobias, DJ, Mar, W, Blasie, JK, Klein, ML (1996) Biophys J 71, 2933.
11. Sprik, M (1993) In Computer simulation in chemical physics. Eds. Allen, MP, Tildesley, DJ. NATO ASI Series, vol. 397, Kluwer, Dordrecht.
12. Tu, K, Tobias, DJ, Klein, ML (1995) J Phys Chem 99, 10035.
13. Williams, DE (1967) J Chem Phys 47, 4680.
14. Ryckaert, JP, Bellemans, A (1978) J Chem Soc Faraday Trans 66, 95.
15. Hammonds, KD, McDonald, IR, Ryckaert, JP (1993) Chem Phys Lett 213, 27.
16. Smith, JC, Karplus, M (1992) J Am Chem Soc 114, 801.
17. Kaminsky, G, Duffy, EM, Matsui, T, Jorgensen, WL (1994) J Phys Chem 98, 13077.
18. Schlenkrich, MJ, Brickmann, J, MacKerell Jr, AD, Karplus, M (1996) In Biological membranes, a molecular perspective from computation and experiment. Eds. Merz, KM Jr, Roux, B. Birkhauser, Boston.
19. Stouch, TR, Ward, KB, Altieri, A, Hagler, AT (1991) J Comp Chem 12, 1033.
20. Tuckerman, ME, Martyna, GJ, Berne, BJ (1990) J Chem Phys 97, 1990.
21. Martyna, GJ, Tuckerman, ME, Tobias, DJ, Klein, ML (1996) Mol Phys 87, 1117.
22. Röthlisberger, U, Klein, ML (1994) Chem Phys Lett 221, 390.
23. Herrebout, WA, van der Veken, BJ, Wang, A, Durig, JR (1995) J Phys Chem 99, 578.
24. Smith, GD, Jaffe, RL (1996) J Phys Chem 100, 18718.
25. Tu, K, Tobias, DJ, Klein, ML (1996) Biophys J 70, 595.
26. Tobias, DJ, Tu, K, Klein, ML (1996) In Monte Carlo and molecular dynamics of condensed matter systems. Eds. Binder, K, Ciccotti, G. Conference proceedings, vol. 49, SIF, Bologna.
27. Williams, DE, Stouch, TR (1993) J Comp Chem 14, 1066.
28. MacKerell Jr, AD (1997) J Chim Phys (this issue).
29. Berendsen, HJC, Grigera, JR, and Straatsma, TP (1987) J Phys Chem 91, 6269.
30. Jorgensen, WL, Chandrasekhar, J, Madura, JD, Impey, RW, Klein, ML (1983) J Chem Phys 79, 926.
31. Martyna, GJ, Tobias, DJ, Klein, ML (1994) J Chem Phys 101, 4177.
32. Ciccotti, G, Ryckaert, JP (1986) Comput Phys Rep 4, 345.
33. Ryckaert, JP, Ciccotti, G, Berendsen, HJC (1977) J Comp Phys 23, 327.
34. Martyna, GJ, Klein, ML, Tuckerman, ME (1992) J Chem Phys 97, 2635.
35. Allen, MP, Tildesley, DJ (1989) Computer simulation of liquids. Oxford University Press, New York.
36. Brooks, BR, Bruccoleri, RE, Olafson, BD, States, DJ, Swaminathan, S, Karplus, M (1983) J Comp Chem 4, 187.
37. Mathisen, H, Norman, N, Pedersen, BF (1967) Acta Chem Scand 21, 9.
38. Smith, AE (1953) J Chem Phys 21, 2229.
39. Habenschuss, A., Narten, AH (1989) J Chem Phys 91, 4299.
40. Abrahamsson, S, Pascher, I (1966) Acta Cryst 21, 79.
41. Sarma, R, Ramirez, F, Narayanan, P, McKeever, B, Okazaki, H, Maracek, JF (1978) J Am Chem Soc 100, 4453.
42. Pascher, I, Sundell, S (1981) J Mol Biol 153, 791.
43. Bonham, RA, Bartell, LS, Kohl, DA (1959) J Am Chem Soc 81, 4765.
44. Fitzwater, S, Bartell, LS (1976) J Am Chem Soc 98, 8338.
45. Habenschuss, A, Narten, AH (1990) J Chem Phys 92, 5692.
46. Harris, KR, Alexander, JJ, Goscinska, T, Malhotra, R, Woolf, LA, Dymond, JH (1993) Mol Phys 78, 235.