Influence of cut-off truncation and artificial periodicity of electrostatic interactions in molecular simulations of solvated ions: A continuum electrostatics study

Journal of Chemical Physics

Volumn 119, Issue 17, 2003, Pages 9129-9144

  Bergdorf, Michael ^a   Peter, Christine ^a   Hünenberger, Philippe H ^a  

^a ETH ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; BOUNDARY CONDITIONS; COMPUTER SIMULATION; ELECTROSTATICS; IONS; MOLECULES; PERMITTIVITY; PERTURBATION TECHNIQUES; SOLVENTS;

ARTIFICIAL PERIODICITY; CUT-OFF TRUNCATION;

CONTINUUM MECHANICS;

EID: 0344898983     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.1614202     Document Type: Article

References (96)

1. M. Karplus and J. A. McCammon, Nat. Struct. Biol. 9, 646 (2002).
2. X. Daura, A. Glättli, P. Gee, C. Peter, and W. F. van Gunsteren, Adv. Protein Chem. 62, 341 (2002).
3. T. E. Cheatham, III and P. A. Kollman, Annu. Rev. Phys. Chem. 51, 435 (2000).
4. L. Saiz, S. Bandyopadhyay, and M. L. Klein, Biosci Rep. 22, 151 (2002).
5. S. B. Engelsen, C. Monteiro, C. Hervé de Penhoat, and S. Pérez, Biophys. Chem. 93, 103 (2001).
6. W. F. van Gunsteren and H. J. C. Berendsen, Angew. Chem., Int. Ed. Engl. 29, 992 (1990).
7. M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids (Oxford University Press, New York, 1987).
8. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus, J. Comput. Chem. 4, 187 (1983).
9. C. L. Brooks III, B. M. Pettitt, and M. Karplus, J. Chem. Phys. 83, 5897 (1985).
10. K. S. Kim, Chem. Phys. Lett. 156, 261 (1989).
11. R. J. Loncharich and B. R. Brooks, Proteins: Struct., Funct., Genet. 6, 32 (1989).
12. P. J. Steinbach and B. R. Brooks, J. Comput. Chem. 15, 667 (1994).
13. J. Norberg and L. Nilsson, Biophys. J. 79, 1537 (2000).
14. J. A. Barker and R. O. Watts, Mol. Phys. 26, 789 (1973).
15. I. G. Tironi, R. Sperb, P. E. Smith, and W. F. van Gunsteren, J. Chem. Phys. 102, 5451 (1995).
16. P. H. Hünenberger and W. F. van Gunsteren, J. Chem. Phys. 108, 6117 (1998).
17. G. Hummer and D. M. Soumpasis, Phys. Rev. E 49. 591 (1994).
18. G. Hummer and D. M. Soumpasis, J. Phys.: Condens. Matter 6, A141 (1994).
19. G. Hummer, L. R. Pratt, and A. E. Garcia, J. Phys. Chem. 100, 1206 (1996).
20. P. P. Ewald, Ann. Phys. (Leipzig) 64, 253 (1921).
21. R. W. Hockney and J. W. Eastwood, Computer Simulation Using Particles (Institute of Physics, Bristol, 1981).
22. T. Darden, D. York, and L. Pedersen, J. Chem. Phys. 98, 10089 (1993).
23. U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee, and L. G. Pedersen, J. Chem. Phys. 103, 8577 (1995).
24. M. Neumann, Mol. Phys. 50, 841 (1983).
25. M. Neumann, O. Steinhauser, and G. S. Pawley, Mol. Phys. 52, 97 (1984).
26. R. H. Wood, J. Chem. Phys. 103, 6177 (1995).
27. N. A. Baker, P. H. Hünenberger, and J. A. McCammon, J. Chem. Phys. 110, 10679 (1999).
28. N. A. Baker, P. H. Hünenberger, and J. A. McCammon, J. Chem. Phys. 113, 2510 (1999).
29. C. L. Brooks III, J. Phys. Chem. 90, 6680 (1986).
30. C. L. Brooks III, J. Chem. Phys. 86, 5156 (1987).
31. J. D. Madura and B. M. Pettitt, Chem. Phys. Lett. 150, 105 (1988).
32. T. P. Straatsma and H. J. C. Berendsen, J. Chem. Phys. 89, 5876 (1988).
33. S. G. Kalko, G. Sese, and J. A. Padro, J. Chem. Phys. 104, 9578 (1996).
34. H. Resat and J. A. McCammon, J. Chem. Phys. 104, 7645 (1996).
35. H. Resat and J. A. McCammon, J. Chem. Phys. 108, 9617 (1998).
36. B. M. Pettitt and P. J. Rossky, J. Chem. Phys. 84, 5836 (1986).
37. L. X. Dang and B. M. Pettitt, J. Phys. Chem. 94, 4303 (1990).
38. E. Guàrdia, R. Rey, and J. A. Padró, J. Chem. Phys. 95, 2823 (1991).
39. L. X. Dang, B. M. Pettitt, and P. J. Rossky, J. Chem. Phys. 96, 4046 (1992).
40. G. Hummer, D. M. Soumpasis, and M. Neumann, Mol. Phys. 81, 1155 (1994).
41. J. S. Bader and D. Chandler, J. Phys. Chem. 96, 6423 (1992).
42. R. A. Friedman and M. Mezei, J. Chem. Phys. 102, 419 (1994).
43. G. S. Del Buono, F. E. Figueirido, and R. M. Levy, Chem. Phys. Lett. 263, 521 (1996).
44. X. Rozanska and C. Chipot, J. Chem. Phys. 112, 9691 (2000).
45. H. Schreiber and O. Steinhauser, Biochemistry 31, 5856 (1992).
46. H. Schreiber and O. Steinhauser, Chem. Phys. 168, 75 (1992).
47. H. Schreiber and O. Steinhauser, J. Mol. Biol. 228, 909 (1992).
48. P. E. Smith and B. M. Pettitt, J. Chem. Phys. 95, 8430 (1991).
49. G. S. Del Buono, T. S. Cohen, and P. J. Rossky, J. Mol. Liq. 60, 221 (1994).
50. L. Perera, U. Essmann, and M. L. Berkowitz, J. Chem. Phys. 102, 450 (1994).
51. S. Boresch and O. Steinhauser, J. Chem. Phys. 115, 10780 (2001).
52. P. H. Hünenberger, in Simulation and Theory of Electrostatic Interactions in Solution: Computational Chemistry, Biophysics, and Aqueous Solution, edited by G. Hummer and L. R. Pratt (American Institute of Physics, New York, 1999), pp. 17-83.
53. M. Deserno and C. Holm, J. Chem. Phys. 109, 7678 (1998).
54. M. Deserno and C. Holm, J. Chem. Phys. 109, 7694 (1998).
55. G. Hummer, L. R. Pratt, and A. E. Garcia, J. Phys. Chem. A 102, 7885 (1998).
56. M. Kastenholz and P. H. Hünenberger, J. Phys. Chem B (to be published).
57. P. H. Hünenberger and J. A. McCammon, J. Chem. Phys. 110, 1856 (1999).
58. P. H. Hünenberger and J. A. McCammon, Biophys. Chem. 78, 69 (1999).
59. W. Weber, P. H. Hünenberger, and J. A. McCammon, J. Phys. Chem. B 104, 3668 (2000).
60. C. Peter, W. F. van Gunsteren, and P. H. Hünenberger, J. Chem. Phys. (to be published).
61. S. Boresch and O. Steinhauser, J. Chem. Phys. 111, 8271 (1999).
62. S. Boresch and O. Steinhauser, J. Chem. Phys. 115, 10793 (2001).
63. M. Marchi, D. Borgis, N. Levy, and P. Ballone, J. Chem. Phys. 114, 4377 (2001).
64. C. Peter, W. F. van Gunsteren, and P. H. Hünenberger, J. Chem. Phys. 116, 7434 (2002).
65. J. D. Madura, M. E. Davis, M. K. Gilson, R. C. Wade, B. A. Luty, and J. A. McCammon, in Reviews in Computational Chemistry, Vol. 4, edited by K. B. Lipkowitz and D. B. Boyd (VCH, New York, 1994), pp. 229-267.
66. B. Honig, K. Sharp, and A.-S. Yang, J. Phys. Chem. 97, 1101 (1993).
67. M. K. Gilson, Curr. Opin. Struct. Biol. 5, 216 (1995).
68. B. Honig and A. Nicholls, Science 268, 1144 (1995).
69. F. Figueirido, G. S. Del Buono, and R. M. Levy, J. Phys. Chem. B 101, 5622 (1997).
70. G. Hummer, L. R. Pratt, and A. E. Garcia, J. Chem. Phys. 107, 9275 (1997).
71. S. Sakane, H. S. Ashbaugh, and R. H. Wood, J. Phys. Chem. B 102, 5673 (1998).
72. G. Hummer, L. R. Pratt, A. E. Garcia, B. J. Berne, and S. W. Rick, J. Phys. Chem. B 101, 3017 (1997).
73. H. S. Ashbaugh and R. H. Wood, J. Chem. Phys. 106, 8135 (1997).
74. J. Åqvist and T. Hansson, J. Phys. Chem. B 102, 3837 (1998).
75. H. S. Ashbaugh and R. H. Wood, J. Phys. Chem. B 102, 3844 (1998).
76. G. Hummer, L. R. Pratt, A. E. Garcia, S. Garde, B. J. Berne, and S. W. Rick, J. Phys. Chem. B 102, 3841 (1998).
77. Y. N. Vorobjev and J. Hermans, J. Phys. Chem. 103, 10234 (1999).
78. T. Darden, D. Pearlman, and L. G. Pedersen, J. Chem. Phys. 109, 10921 (1998).
79. Y. Y. Sham and A. Warshel, J. Chem. Phys. 109, 7940 (1998).
80. H. Resat, M. Mezei, and J. A. McCammon, J. Phys. Chem. 100, 1426 (1996).
81. F. Figueirido, G. S. Del Buono, and R. M. Levy, J. Chem. Phys. 103, 6133 (1995).
82. L. R. Pratt, G. Hummer, and A. E. Garciá, Biophys. Chem. 51, 147 (1994).
83. A. Kovalenko and F. Hirata, J. Chem. Phys. 112, 10403 (2000).
84. A. Masunov and T. Lazaridis, J. Am. Chem. Soc. 125, 1722 (2003).
85. M. Neumann and O. Steinhauser, Mol. Phys. 57, 97 (1986).
86. M. Born, Z. Phys. 1, 45 (1920).
87. J.-C. Soetens, C. Millot, C. Chipot, G. Jansen, J. G. Ángyán, and B. Maigret, J. Phys. Chem. B 101, 10910 (1997).
88. L. Degrève and F. L. B. da Silva, J. Chem. Phys. 110, 3070 (1999).
89. D. Sardella Vieira and L. Degrève, J. Mol. Struct. 580, 127 (2002).
90. G. Hummer, D. M. Soumpasis, and M. Neumann, Mol. Phys. 77, 769 (1992).
91. C. Satheesan Babu, P.-K. Yang, and C. Lim, J. Biol. Phys. 28, 95 (2002).
92. W. F. van Gunsteren, S. R. Billeter, A. A. Eising, P. H. Hünenberger, P. Krüger, A. E. Mark, W. R. P. Scott, and I. G. Tironi, Biomolecular Simulation: The GROMOS96 Manual and User Guide (Verlag der Fachvereine, Zürich, 1996).
93. H. J. C. Berendsen, D. van der Spoel, and R. van Drunen, Comput. Phys. Commun. 91, 43 (1995).
94. L. Onsager, J. Am. Chem. Soc. 58, 1486 (1936).
95. J. Warwicker and H. C. Watson, J. Mol. Biol. 157, 671 (1982).
96. P. Auffinger and D. L. Beveridge, Chem. Phys. Lett. 234, 413 (1995).