An image-based reaction field method for electrostatic interactions in molecular dynamics simulations of aqueous solutions

Journal of Chemical Physics

Volumn 131, Issue 15, 2009, Pages

  Lin, Yuchun ^a   Baumketner, Andrij ^a   Deng, Shaozhong ^a   Xu, Zhenli ^a   Jacobs, Donald ^a   Cai, Wei ^a  

^a UNIVERSITY OF NORTH CAROLINA AT CHARLOTTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AQUEOUS SOLUTIONS; COMPUTATIONAL COSTS; DIELECTRIC CONTINUUM; DYNAMIC PROPERTY; ELECTROLYTE SOLUTIONS; ELECTROSTATIC INTERACTIONS; ELECTROSTATIC POTENTIALS; EXPLICIT SOLVENTS; EXPLICIT WATER; FAST MULTIPOLE METHOD; FUTURE APPLICATIONS; IMAGE CHARGES; IMAGE-BASED; IMAGE-CHARGE METHOD; IMPLICIT SOLVENTS; LATTICE SUM; LIQUID WATER; MODEL PARAMETERS; MOLECULAR DYNAMICS SIMULATIONS; OPTIMAL SETS; PERIODIC BOUNDARY CONDITIONS; PURE WATER; REACTION FIELDS; SOLUTE MOLECULES; SOLVATED BIOMOLECULES; SOLVATION MODELS; SPHERICAL CAVITIES; SURFACE EFFECT;

BIOMOLECULES; COMPUTATIONAL EFFICIENCY; COMPUTER CRIME; ELECTROLYTES; ELECTROSTATICS; IMAGE STORAGE TUBES; MOLECULAR DYNAMICS; REACTION KINETICS; SOLUTIONS; SOLVENTS;

SIMULATORS;

WATER;

ARTICLE; CHEMISTRY; MOLECULAR DYNAMICS; SOLUTION AND SOLUBILITY; STATIC ELECTRICITY;

MOLECULAR DYNAMICS SIMULATION; SOLUTIONS; STATIC ELECTRICITY; WATER;

EID: 70449377178     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3245232     Document Type: Article

References (99)

1. C. Sagui and T. A. Darden, Annu. Rev. Biophys. Biomol. Struct. 1056-8700 28, 155 (1999). 10.1146/annurev.biophys.28.1.155 (Pubitemid 29319256)
2. M. E. Davis and J. A. McCammon, Chem. Rev. (Washington, D.C.) 0009-2665 90, 509 (1990). 10.1021/cr00101a005
3. A. Warshel and S. T. Russell, Q. Rev. Biophys. 0033-5835 17, 283 (1984). 10.1017/S0033583500005333
4. P. Koehl, Curr. Opin. Struct. Biol. 0959-440X 16, 142 (2006). 10.1016/j.sbi.2006.03.001
5. W. F. van Gunsteren and J. J. C. Berendsen, Angew. Chem., Int. Ed. Engl. 0570-0833 29, 992 (1990). 10.1002/anie.199009921
6. T. Simonson, Rep. Prog. Phys. 0034-4885 66, 737 (2003). 10.1088/0034-4885/66/5/202 (Pubitemid 36685137)
7. W. F. van Gunsteren, F. J. Luque, D. Timms, and A. E. Torda, Annu. Rev. Biophys. Biomol. Struct. 1056-8700 23, 847 (1994). 10.1146/annurev.bb.23.060194. 004215
8. C. J. Cramer and D. G. Truhlar, Chem. Rev. (Washington, D.C.) 0009-2665 99, 2161 (1999). 10.1021/cr960149m
9. C. Moser, J. Keske, K. Warncke, R. Farid, and P. Dutton, Nature (London) 0028-0836 355, 796 (1992). 10.1038/355796a0
10. H. Nakamura, Q. Rev. Biophys. 0033-5835 29, 1 (1996). 10.1017/S0033583500005746
11. R. Zhou, Proteins 0887-3585 53, 148 (2003). 10.1002/prot.10483 (Pubitemid 37193811)
12. A. Warshel, P. K. Sharma, M. Kato, Y. Xiang, H. Liu, and M. H. M. Olsson, Chem. Rev. (Washington, D.C.) 0009-2665 106, 3210 (2006). 10.1021/cr0503106 (Pubitemid 44376933)
13. B. Roux, Implicit Solvent Models, Computational Biochemistry and Biophysics (Marcel Dekker, New York, 2001).
14. B. Honig and A. Nicholls, Science 0036-8075 268, 1144 (1995). 10.1126/science.7761829
15. N. A. Baker, Curr. Opin. Struct. Biol. 0959-440X 15, 137 (2005). 10.1016/j.sbi.2005.02.001
16. J. Wang, C. H. Tan, Y. H. Tan, Q. Lu, and R. Luo, Comm. Comp. Phys 3, 1010 (2008).
17. J. Warwicker and H. C. Watson, J. Mol. Biol. 0022-2836 157, 671 (1982). 10.1016/0022-2836(82)90505-8
18. M. Holst and F. Saied, J. Comput. Chem. 0192-8651 14, 105 (1993). 10.1002/jcc.540140114
19. R. Luo, L. David, and M. K. Gilson, J. Comput. Chem. 0192-8651 23, 1244 (2002). 10.1002/jcc.10120 (Pubitemid 35009216)
20. W. H. Orttung, Ann. N.Y. Acad. Sci. 0077-8923 303, 22 (1977). 10.1111/j.1749-6632.1977.tb55916.x
21. M. J. Holst, N. A. Baker, and F. Wang, J. Comput. Chem. 0192-8651 21, 1319 (2000). 10.1002/1096-987X(20001130)21:15<1319::AID-JCC1>3.0.CO;2-8
22. L. Chen, M. J. Holst, and J. C. Xu, SIAM (Soc. Ind. Appl. Math.) J. Numer. Anal. 0036-1429 45, 2298 (2007). 10.1137/060675514
23. D. Xie and S. Zhou, BIT Numerical Mathematics 47, 853 (2007). 0006-3835 10.1007/s10543-007-0145-9
24. D. G. Levitt, Biophys. J. 0006-3495 22, 209 (1978). 10.1016/S0006- 3495(78)85485-X
25. Y. N. Vorobjev and H. A. Scheraga, J. Comput. Chem. 0192-8651 18, 569 (1997). 10.1002/(SICI)1096-987X(199703)18:4<569::AID-JCC10>3.0.CO;2-B
26. A. H. Boschitsch, M. O. Fenley, and H. X. Zhou, J. Phys. Chem. B 1089-5647 106, 2741 (2002). 10.1021/jp013607q (Pubitemid 35275953)
27. B. Z. Lu, X. L. Cheng, J. F. Huang, and J. A. McCammon, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 103, 19314 (2006). 10.1073/pnas.0605166103 (Pubitemid 46026029)
28. M. Feig and C. L. Brooks III, Curr. Opin. Struct. Biol. 0959-440X 14, 217 (2004). 10.1016/j.sbi.2004.03.009 (Pubitemid 38495800)
29. Q. Lu and R. Luo, J. Chem. Phys. 0021-9606 119, 11035 (2003). 10.1063/1.1622376
30. W. Im, D. Beglov, and B. Roux, Comput. Phys. Commun. 0010-4655 111, 59 (1998). 10.1016/S0010-4655(98)00016-2
31. M. Feig, A. Onufriev, M. S. Lee, W. Im, D. A. Case, and C. L. Brooks III, J. Comput. Chem. 0192-8651 25, 265 (2004). 10.1002/jcc.10378
32. R. Blaak and J. P. Hansen, J. Chem. Phys. 0021-9606 124, 144714 (2006). 10.1063/1.2185092
33. J. Dai, I. Tsukerman, A. Rubinstein, and S. Sherman, IEEE Trans. Magn. 0018-9464 43, 1217 (2007). 10.1109/TMAG.2006.890959 (Pubitemid 46495446)
34. Z. Yu, M. P. Jacobson, C. S. Rapp, and R. A. Friesner, J. Phys. Chem. B 1089-5647 108, 6643 (2004). 10.1021/jp037821l
35. M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids (Oxford University Press, Oxford, 1987).
36. P. Ewald, Ann. Phys. 0003-3804 369, 253 (1921). 10.1002/andp.19213690304
37. R. Abagyan and M. Totrov, J. Mol. Biol. 0022-2836 235, 983 (1994). 10.1006/jmbi.1994.1052 (Pubitemid 24047836)
38. T. A. Darden, D. M. York, and L. G. Pedersen, J. Chem. Phys. 0021-9606 98, 10089 (1993). 10.1063/1.464397
39. U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee, and L. Pedersen, J. Chem. Phys. 0021-9606 103, 8577 (1995). 10.1063/1.470117
40. J. Shimada, H. Kaneko, and T. Takada, J. Comput. Chem. 0192-8651 14, 867 (1993). 10.1002/jcc.540140712
41. B. A. Luty, M. E. Davis, I. G. Tironi, and W. F. van Gunsteren, Mol. Simul. 0892-7022 14, 11 (1994). 10.1080/08927029408022004
42. L. Greengard and V. Rokhlin, J. Comput. Phys. 0021-9991 73, 325 (1987). 10.1016/0021-9991(87)90140-9
43. L. Greengard, The Rapid Evaluation of Potential Fields in Particle Systems (MIT Press, Cambridge, 1988).
44. W. Weber, P. H. Hunenberger, and J. A. McCammon, J. Phys. Chem. B 1089-5647 104, 3668 (2000). 10.1021/jp9937757 (Pubitemid 30858506)
45. M. A. Villarreal and G. G. Montich, J. Biomol. Struct. Dyn. 0739-1102 23, 135 (2005).
46. M. A. Kastenholz and P. H. Hünenberger, J. Phys. Chem. B 1089-5647 108, 774 (2004). 10.1021/jp0350924
47. S. Balasubramanian, C. J. Mundy, and M. L. Klein, J. Chem. Phys. 0021-9606 105, 11190 (1996). 10.1063/1.472918
48. M. Belhadj, H. E. Alper, and R. M. Levy, Chem. Phys. Lett. 0009-2614 179, 13 (1991). 10.1016/0009-2614(91)90284-G
49. P. H. Hunenberger and J. A. McCammon, Biophys. Chem. 0301-4622 78, 69 (1999). 10.1016/S0301-4622(99)00007-1 (Pubitemid 29206658)
50. A. Okur and C. Simmerling, Annu. Rep. Comp. Chem 2, 97 (2006). 10.1016/S1574-1400(06)02006-8 0301-4622
51. M. S. Lee, Jr., F. R. Salsbury, and M. A. Olson, J. Comput. Chem. 0192-8651 25, 1967 (2004). 10.1002/jcc.20119
52. M. S. Lee and M. A. Olson, J. Phys. Chem. B 1089-5647 109, 5223 (2005). 10.1021/jp046377z (Pubitemid 40407743)
53. W. Im, S. Berǹche, and B. Roux, J. Chem. Phys. 0021-9606 114, 2924 (2001). 10.1063/1.1336570 (Pubitemid 32253408)
54. D. Bashford and D. A. Case, Annu. Rev. Phys. Chem. 0066-426X 51, 129 (2000). 10.1146/annurev.physchem.51.1.129
55. P. K. Yang, S. H. Liaw, and C. Lim, J. Phys. Chem. B 1089-5647 106, 2973 (2002). 10.1021/jp012900n (Pubitemid 35290309)
56. G. King and A. Warshel, J. Chem. Phys. 0021-9606 91, 3647 (1989). 10.1063/1.456845
57. D. Beglov and B. Roux, J. Chem. Phys. 0021-9606 100, 9050 (1994). 10.1063/1.466711
58. H. Alper and R. Levy, J. Chem. Phys. 0021-9606 99, 9847 (1993). 10.1063/1.465468
59. J. G. Kirkwood, J. Chem. Phys. 0021-9606 2, 351 (1934). 10.1063/1.1749489
60. J. G. Kirkwood, Chem. Rev. (Washington, D.C.) 0009-2665 19, 275 (1936). 10.1021/cr60064a007
61. J. C. Maxwell, A Treatise on Electricity and Magnetism (Dover, New York, 1954).
62. H. L. Friedman, Mol. Phys. 0026-8976 29, 1533 (1975). 10.1080/00268977500101341
63. J. J. Havranek and P. B. Harbury, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 96, 11145 (1999). 10.1073/pnas.96.20.11145 (Pubitemid 29487348)
64. J. A. C. Rullmann and P. T. V. Duijnen, Mol. Phys. 0026-8976 61, 293 (1987). 10.1080/00268978700101151
65. A. Wallqvist, Mol. Simul. 0892-7022 10, 13 (1993). 10.1080/ 08927029308022494
66. L. Wang and J. Hermans, J. Phys. Chem. 0022-3654 99, 12001 (1995). 10.1021/j100031a031
67. G. Petraglio, M. Ceccarelli, and M. Parrinello, J. Chem. Phys. 0021-9606 123, 044103 (2005). 10.1063/1.1955449 (Pubitemid 41164715)
68. W. Cai, S. Deng, and D. Jacobs, J. Comput. Phys. 0021-9991 223, 846 (2007). 10.1016/j.jcp.2006.10.019
69. S. Deng and W. Cai, Commun. Comput. Phys. 2, 1007 (2007).
70. S. Deng and W. Cai, J. Comput. Phys. 0021-9991 227, 1246 (2007). 10.1016/j.jcp.2007.09.001
71. A. V. Finkelstein, Mol. Biol. 0026-8933 11, 811 (1977).
72. I. V. Lindell, Radio Sci. 0048-6604 27, 1 (1992). 10.1029/91RS02255
73. C. Neumann, Hydrodynamische untersuchen nebst einem anhang uber die probleme der elektrostatik und der magnetischen induktion (Teubner, Leipzig, 1883), Vol. 279.
74. W. T. Norris, IEE Proc.: Sci., Meas. Technol. 1350-2344 142, 142 (1995). 10.1049/ip-smt:19951564
75. Z. Xu, S. Deng, and W. Cai, J. Comput. Phys. 0021-9991 228, 2092 (2009). 10.1016/j.jcp.2008.11.023
76. J. A. Barker and R. O. Watts, Mol. Phys. 0026-8976 26, 789 (1973). 10.1080/00268977300102101
77. G. Mathias, B. Egwolf, M. Nonella, and P. Tavan, J. Chem. Phys. 0021-9606 118, 10847 (2003). 10.1063/1.1574774
78. I. G. Tironi, R. Sperb, P. E. Smith, and W. F. van Gunsteren, J. Chem. Phys. 0021-9606 102, 5451 (1995). 10.1063/1.469273
79. X. W. Wu and B. R. Brooks, J. Chem. Phys. 0021-9606 122, 044107 (2005). 10.1063/1.1836733 (Pubitemid 41047582)
80. P. H. Hunenberger and W. F. van Gunsteren, J. Chem. Phys. 0021-9606 108, 6117 (1998). 10.1063/1.476022
81. D. van der Spoel, P. J. van Maaren, and H. J. C. Berendsen, J. Chem. Phys. 0021-9606 108, 10220 (1998). 10.1063/1.476482
82. G. Brancato, A. D. Nola, V. Barone, and A. Amadei, J. Chem. Phys. 0021-9606 122, 154109 (2005). 10.1063/1.1877172 (Pubitemid 40858256)
83. J. A. Barker, Mol. Phys. 0026-8976 83, 1057 (1994). 10.1080/ 00268979400101781
84. M. Xiang, S. Deng, and W. Cai, " A sixth-order image approximation to the ionic solvent induced reaction field.," J. Sci. Comput. 0885-7474 (in press).
85. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, J. Chem. Phys. 0021-9606 79, 926 (1983). 10.1063/1.445869
86. L. Ying, G. Biros, and D. Zorin, J. Comput. Phys. 0021-9991 196, 591 (2004). 10.1016/j.jcp.2003.11.021
87. M. Yoneya, H. J. C. Berendsen, and K. Hirasawa, Mol. Simul. 0892-7022 13, 395 (1994). 10.1080/08927029408022001
88. J. T. Slusher and P. T. Cummings, Mol. Simul. 0892-7022 18, 213 (1996). 10.1080/08927029608022360
89. S. Jang and G. A. Voth, Biopolymers 0006-3525 107, 9514 (1997).
90. H. J. C. Berendsen, D. van der Spoel, and R. van Drunen, Comput. Phys. Commun. 0010-4655 91, 43 (1995). 10.1016/0010-4655(95)00042-E
91. E. Lindahl, B. Hess, and D. van der Spoel, J. Mol. Model. 0948-5023 7, 306 (2001).
92. D. van der Spoel, E. Lindahl, B. Hess, A. R. van Buuren, E. Apol, P. J. Meulenhoff, D. P. Tieleman, A. L. T. M. Sijbers, K. A. Feenstra, R. van Drunen, and H. J. C. Berendsen (unpublished).
93. V. Ballenegger and J. P. Hansen, J. Chem. Phys. 0021-9606 122, 114711 (2005). 10.1063/1.1845431
94. L. Onsager, J. Am. Chem. Soc. 0002-7863 58, 1486 (1936). 10.1021/ja01299a050
95. A. Warshel, P. K. Sharma, M. Kato, and W. W. Parson, Biochim. Biophys. Acta. 1764, 1647 (2006). 10.1016/j.bbapap.2006.08.007 1570-9639
96. D. Frenkel and B. Smit, Understanding Molecular Simulation (Academic, London, 2002).
97. H. J. C. Berendsen, " Molecular dynamics and Monte Carlo calculations on water.," CECAM Report No. 29, 1972.
98. D. J. Adams and I. R. McDonald, Mol. Phys. 0026-8976 32, 931 (1976). 10.1080/00268977600102351
99. J. G. Powles, R. F. Fowler, and W. A. B. Evans, Chem. Phys. Lett. 0009-2614 107, 280 (1984). 10.1016/0009-2614(84)85129-5