Accounting for polarization in molecular simulation

Computer Physics Communications

Volumn 172, Issue 2, 2005, Pages 69-85

  Yu, Haibo ^a,b   Van Gunsteren, Wilfred F ^a  

^a ETH ZURICH   (Switzerland)

^b UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

Charge On Spring; Drude oscillator; Fluctuation charges; Molecular dynamics; Polarizable dipole; Polarization; Water

Indexed keywords

COMPUTER SIMULATION; MATHEMATICAL MODELS; MOLECULAR DYNAMICS; MOLECULAR PHYSICS; PERMITTIVITY; POLARIZATION; WATER;

CHARGE-ON-SPRING; DRUDE OSCILLATOR; FLUCTUATION CHARGES; POLARIZABLE DIPOLES;

COMPUTATIONAL METHODS;

EID: 25844474073     PISSN: 00104655     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cpc.2005.01.022     Document Type: Article

References (130)

1. B.K.P. Scaife Principles of Dielectrics 1989 Oxford University Press Oxford, UK
2. J.D. Jackson Classical Electrodynamics third ed. 2001 John Wiley & Sons New York
3. P.H. Hünenberger, and W.F. van Gunsteren Empirical classical interaction functions for molecular simulation W.F. van Gunsteren P.K. Weiner A.J. Wilkinson Computer Simulation of Biomolecular Systems Theoretical and Experimental Applications vol. 3 1997 Kluwer Academic Publishers Dordrecht, The Netherlands 3 82
4. J.W. Ponder, and D.A. Case Adv. Prot. Chem. 66 2003 27
5. R.C. Weast Handbook of Chemistry and Physics 1983 CRC Boca Raton
6. Y.S. Badyal, M.L. Saboungi, D.L. Price, S.D. Shastri, D.R. Haeffner, and A.K. Soper J. Chem. Phys. 112 2000 9206
7. H.J.C. Berendsen, J.R. Grigera, and T.P. Straatsma J. Phys. Chem. 91 1987 6269
8. O.A. Karim Chem. Phys. Lett. 184 1991 560
9. A.D. Buckingham Proc. Roy. Soc. London Ser. A Math. 238 1956 235
10. U. Kaatze J. Chem. Eng. Data 34 1989 371
11. J. Applequist, J.R. Carl, and K.K. Fung J. Am. Chem. Soc. 94 1972 2952
12. B.T. Thole Chem. Phys. 59 1981 341
13. W.F. van Gunsteren, and H.J.C. Berendsen Angew. Chem. Int. Edit. Engl. 29 1990 992
14. T.A. Halgren, and W. Damm Curr. Opin. Struct. Biol. 11 2001 236
15. S.W. Rick, and S.J. Stuart Potentials and algorithms for incorporating polarizability in computer simulations K.B. Lipowitz D.B. Boyd Rev. Comput. Chem. 2002 Wiley-VCH New York 89 154
16. F.J. Vesely J. Comp. Phys. 24 1977 361
17. F.H. Stillinger, and C.W. David J. Chem. Phys. 69 1978 1473
18. P. Barnes, J.L. Finney, J.D. Nicholas, and J.E. Quinn Nature 282 1979 459
19. A. Warshel J. Phys. Chem. 83 1979 1640
20. B. Guillot J. Mol. Liq. 101 2002 219
21. G. Ruocco, and M. Sampoli Mol. Phys. 82 1994 875
22. H.J.C. Berendsen, J.P.M. Postma, W.F. van Gunsteren, and J. Hermans Interaction models for water in relation to protein hydration B. Pullman Intermolecular Forces 1981 Reidel Dordrecht 331 342
23. W.L. Jorgensen J. Am. Chem. Soc. 103 1981 335
24. M. Orozco, and F.J. Luque Chem. Rev. 100 2000 4187
25. V. Daggett, P.A. Kollman, and I.D. Kuntz Biopolymers 31 1991 285
26. J. Zhu, Y.Y. Shi, and H.Y. Liu J. Phys. Chem. B 106 2002 4844
27. A. Warshel, S.T. Russell, and A.K. Churg Proc. Natl. Acad. Sci. USA 81 1984 4785
28. A.R. Srinivasan, and W.K. Olson Fed. Proc. 39 1980 2199
29. B.E. Hingerty, R.H. Ritchie, T.L. Ferrell, and J.E. Turner Biopolymers 24 1985 427
30. J. Ramstein, and R. Lavery Proc. Natl. Acad. Sci. USA 85 1988 7231
31. K.A. Sharp, and B. Honig Annu. Rev. Biophys. Biophys. Chem. 19 1990 301
32. C.N. Schutz, and A. Warshel Proteins 44 2001 400
33. G. King, F.S. Lee, and A. Warshel J. Chem. Phys. 95 1991 4366
34. T. Simonson, D. Perahia, and A.T. Brunger Biophys. J. 59 1991 670
35. H.A. Stern, and S.E. Feller J. Chem. Phys. 118 2003 3401
36. H.J.C. Berendsen, Private communication, 2004
37. R. Clausius Die mechanische Wärmetheorie II 1879 Braunschweig Vieweg
38. O.F. Mossotti, Discussione analitica sull'influenza che l'azione di un mezzo dielettrico ha sulla distribuzione dell'elettricità alla superficie di più corpi elettrici disseminati in esso, in: Mem. Math. Fisica Moderna, vol. XXIV, 1850, pp. 49-74
39. A. Warshel, and M. Levitt J. Mol. Biol. 103 1976 227
40. A. Warshel, and S.T. Russell Q. Rev. Biophys. 17 1984 283
41. S.T. Russell, and A. Warshel J. Mol. Biol. 185 1985 389
42. R.G. Parr, and W.T. Yang Density-Functional Theory of Atoms and Molecules 1989 Oxford University Press New York
43. W. Thiel Semiempirical methods J. Grotendorst Modern Methods and Algorithms in Quantum Chemistry vol. 3 2000 John von Neumann Institute for Computing Jülich 261 283
44. A. Warshel Computer Modelling of Chemical Reactions in Enzyme and Solutions 1991 John Wiley & Sons New York
45. D. Borgis, and A. Staib Chem. Phys. Lett. 238 1995 187
46. J.L. Gao J. Phys. Chem. B 101 1997 657
47. J.L. Gao J. Chem. Phys. 109 1998 2346
48. A.E. Lefohn, M. Ovchinnikov, and G.A. Voth J. Phys. Chem. B 105 2001 6628
49. M.J. Field, P.A. Bash, and M. Karplus J. Comput. Chem. 11 1990 700
50. J. Åqvist, and A. Warshel Chem. Rev. 93 1993 2523
51. J.L. Gao Methods and applications of combined quantum mechanical and molecular mechanical potentials K.B. Lipowitz D.B. Boyd Rev. Comput. Chem. vol. 7 1996 VCH Publishers New York 119 185
52. D. Bakowies, and W. Thiel J. Phys. Chem. 100 1996 10580
53. V. Gogonea, D. Suarez, A. van der Vaart, and K.M. Merz Curr. Opin. Struct. Biol. 11 2001 217
54. P. Bandyopadhyay, and M.S. Gordon J. Chem. Phys. 113 2000 1104
55. L. Gontrani, B. Mennucci, and J. Tomasi Theochem - J. Mol. Struct. 500 2000 113
56. T. Vreven, B. Mennucci, C.O. da Silva, K. Morokuma, and J. Tomasi J. Chem. Phys. 115 2001 62
57. P. Bandyopadhyay, M.S. Gordon, B. Mennucci, and J. Tomasi J. Chem. Phys. 116 2002 5023
58. Q. Cui J. Chem. Phys. 117 2002 4720
59. D. van Belle, I. Couplet, M. Prevost, and S.J. Wodak J. Mol. Biol. 198 1987 721
60. R.S. Mulliken J. Chem. Phys. 2 1934 782
61. R.G. Parr, and R.G. Pearson J. Am. Chem. Soc. 105 1983 7512
62. A.K. Rappé, and W.A. Goddard J. Phys. Chem. 95 1991 3358
63. S.W. Rick, S.J. Stuart, and B.J. Berne J. Chem. Phys. 101 1994 6141
64. J.L. Banks, G.A. Kaminski, R.H. Zhou, D.T. Mainz, B.J. Berne, and R.A. Friesner J. Chem. Phys. 110 1999 741
65. S. Patel, and C.L. Brooks J. Comput. Chem. 25 2004 1
66. S. Patel, A.D. MacKerell, and C.L. Brooks J. Comput. Chem. 25 2004 1504
67. P. Drude The Theory of Optics 1902 Longmans, Green, and Co. New York
68. M. Born, and K. Huang Dynamic Theory of Crystal Lattices 1954 Oxford University Press Oxford, UK
69. T.P. Straatsma, and J.A. McCammon Mol. Simulation 5 1990 181
70. B.G. Dick, and A.W. Overhauser Phys. Rev. 112 1958 90
71. J.S. Cao, and B.J. Berne J. Chem. Phys. 99 1993 6998
72. P.C. Jordan, P.J. van Maaren, J. Mavri, D. van der Spoel, and H.J.C. Berendsen J. Chem. Phys. 103 1995 2272
73. N.H. de Leeuw, and S.C. Parker Phys. Rev. B 58 1998 13901
74. P.J. van Maaren, and D. van der Spoel J. Phys. Chem. B 105 2001 2618
75. H.B. Yu, T. Hansson, and W.F. van Gunsteren J. Chem. Phys. 118 2003 221
76. G. Lamoureux, A.D. MacKerell, and B. Roux J. Chem. Phys. 119 2003 5185
77. S.J. Stuart, and B.J. Berne J. Phys. Chem. 100 1996 11934
78. H. Saint-Martin, J. Hernandez-Cobos, M.I. Bernal-Uruchurtu, I. Ortega-Blake, and H.J.C. Berendsen J. Chem. Phys. 113 2000 10899
79. B. Hess, H. Saint-Martin, and H.J.C. Berendsen J. Chem. Phys. 116 2002 9602
80. H. Saint-Martin, B. Hess, and H.J.C. Berendsen J. Chem. Phys. 120 2004 11133
81. H.A. Stern, G.A. Kaminski, J.L. Banks, R.H. Zhou, B.J. Berne, and R.A. Friesner J. Phys. Chem. B 103 1999 4730
82. A.J. Stone Mol. Phys. 56 1985 1065
83. J.R. Maple, and C.S. Ewig J. Chem. Phys. 115 2001 4981
84. W.F. Murphy J. Chem. Phys. 67 1977 5877
85. J. Caldwell, L.X. Dang, and P.A. Kollman J. Am. Chem. Soc. 112 1990 9144
86. E. Neufeld, H.B. Yu, T. Hansson, W.F. van Gunsteren, Polarizable water models and dielectric permittivity, Semester Project, 2003
87. O. Engkvist, P.O. Åstrand, and G. Karlström J. Phys. Chem. 100 1996 6950
88. P.Y. Ren, and J.W. Ponder J. Comput. Chem. 23 2002 1497
89. U. Dinur, and A.T. Hagler J. Comput. Chem. 16 1995 154
90. U. Koch, and A.J. Stone J. Chem. Soc.-Faraday Trans. 92 1996 1701
91. J.W. Caldwell, and P.A. Kollman J. Phys. Chem. 99 1995 6208
92. C.J. Burnham, J.C. Li, S.S. Xantheas, and M. Leslie J. Chem. Phys. 110 1999 4566
93. T.C. Beutler, A.E. Mark, R.C. van Schaik, P.R. Gerber, and W.F. van Gunsteren Chem. Phys. Lett. 222 1994 529
94. W. Damm, W.F. van Gunsteren, Unpublished results, 2000
95. G.A. Kaminski, H.A. Stern, B.J. Berne, and R.A. Friesner J. Phys. Chem. A 108 2004 621
96. P. Ahlström, A. Wallqvist, S. Engström, and B. Jönsson Mol. Phys. 68 1989 563
97. M. Sprik J. Phys. Chem. 95 1991 2283
98. D. van Belle, M. Froeyen, G. Lippens, and S.J. Wodak Mol. Phys. 77 1992 239
99. D. van Belle, and S.J. Wodak Comput. Phys. Comm. 91 1995 253
100. D.E. Williams J. Comput. Chem. 9 1988 745
101. J.A. Barker, and R.O. Watts Mol. Phys. 26 1973 789
102. I.G. Tironi, R. Sperb, P.E. Smith, and W.F. van Gunsteren J. Chem. Phys. 102 1995 5451
103. P.P. Ewald Ann. Phys. 64 1921 253
104. R.W. Hockney, and J.W. Eastwood Computer Simulation Using Particles second ed. 1988 Institute of Physics Publishing Bristol, UK
105. T. Darden, D. York, and L. Pedersen J. Chem. Phys. 98 1993 10089
106. T.M. Nymand, and P. Linse J. Chem. Phys. 112 2000 6386
107. P.Y. Ren, and J.W. Ponder J. Phys. Chem. B 107 2003 5933
108. A. Toukmaji, C. Sagui, J. Board, and T. Darden J. Chem. Phys. 113 2000 10913
109. H.J.C. Berendsen, D. van der Spoel, and R. van Drunen Comput. Phys. Comm. 91 1995 43
110. E. Lindahl, B. Hess, and D. van der Spoel J. Mol. Model. 7 2001 306
111. 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 GROMOS Manual and User Guide 1996 vdf Hochschulverlag, ETH Zürich, Switzerland
112. W.R.P. Scott, P.H. Hünenberger, I.G. Tironi, A.E. Mark, S.R. Billeter, J. Fennen, A.E. Torda, T. Huber, P. Krüger, and W.F. van Gunsteren J. Phys. Chem. A 103 1999 3596
113. H.B. Yu, and W.F. van Gunsteren J. Chem. Phys. 121 2004 9549
114. B.R. Brooks, R.E. Bruccoleri, B.D. Olafson, D.J. States, S. Swaminathan, and M. Karplus J. Comput. Chem. 4 1983 187
115. J.G. Kirkwood J. Chem. Phys. 3 1935 300
116. J. Hasted Liquid water: Dielectric properties F. Franks Water, A Comprehensive Treatise 1972 Plenum Press New York 255 309
117. P.L. Silvestrelli, and M. Parrinello J. Chem. Phys. 111 1999 3572
118. S.A. Clough, Y. Beers, G.P. Klein, and L.S. Rothman J. Chem. Phys. 59 1973 2254
119. G. Maroulis Chem. Phys. Lett. 289 1998 403
120. J. Verhoeve, and A. Dymanus J. Chem. Phys. 52 1970 3222
121. J.A. Odutola, and T.R. Dyke J. Chem. Phys. 72 1980 5062
122. W. Klopper, J.G.C.M. van Duijneveldt-van de Rijdt, and F.B. van Duijneveldt Phys. Chem. Chem. Phys. 2 2000 2227
123. L.A. Curtiss, D.J. Frurip, and M. Blander J. Chem. Phys. 71 1979 2703
124. J.K. Gregory, D.C. Clary, K. Liu, M.G. Brown, and R.J. Saykally Science 275 1997 814
125. 2O, PhD thesis, Rijksuniversiteit, Groningen, The Netherlands, 1985
126. K. Krynicki, C.D. Green, and D.W. Sawyer Faraday Discuss. 66 1978 199
127. K. Laasonen, M. Sprik, M. Parrinello, and R. Car J. Chem. Phys. 99 1993 9080
128. H.M. Lee, S.B. Suh, J.Y. Lee, P. Tarakeshwar, and K.S. Kim J. Chem. Phys. 112 2000 9759
129. K. Liu, M.G. Brown, and R.J. Saykally J. Phys. Chem. A 101 1997 8995
130. E.R. Batista, S.S. Xantheas, and H. Jönsson J. Chem. Phys. 111 1999 6011