Treecode algorithm for pairwise electrostatic interactions with solvent-solute polarization

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Volumn 81, Issue 2, 2010, Pages

  Xu, Zhenli ^a,b  

^a SHANGHAI JIAO TONG UNIVERSITY   (China)

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

Author keywords

[No Author keywords available]

Indexed keywords

BIOMOLECULAR SIMULATION; ELECTROSTATIC FREE ENERGY; ELECTROSTATIC INTERACTIONS; EXPANSION COEFFICIENTS; GENERALIZED BORN; MACROSCOPIC SOLVENTS; MULTIPOLE EXPANSIONS; NUMERICAL TESTS; PAIRWISE INTERACTION; POLARIZATION EFFECT; POLARIZATION FUNCTIONS; REACTION POTENTIAL; SPATIAL DIFFERENCES; TREE-CODE ALGORITHM;

ELECTROSTATICS; POLARIZATION;

SOLVENTS;

EID: 76749157846     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.81.020902     Document Type: Article

References (31)

1. A. Appel, SIAM J. Sci. Comput. (USA) 6, 85 (1985). 10.1137/0906008
2. J. Barnes and P. Hut, Nature (London) 324, 446 (1986). 10.1038/324446a0
3. L. Greengard and V. Rokhlin, J. Comput. Phys. 73, 325 (1987). 10.1016/0021-9991(87)90140-9
4. L. Greengard, The Rapid Evaluation of Potential Fields in Particle Systems (MIT, Cambridge, 1987).
5. Z. H. Duan and R. Krasny, J. Chem. Phys. 113, 3492 (2000). 10.1063/1.1289918
6. H. Cheng, L. Greengard, and V. Rokhlin, J. Comput. Phys. 155, 468 (1999). 10.1006/jcph.1999.6355
7. L. Ying, G. Biros, and D. Zorin, J. Comput. Phys. 196, 591 (2004). 10.1016/j.jcp.2003.11.021
8. B. Shanker and H. Huang, J. Comput. Phys. 226, 732 (2007). 10.1016/j.jcp.2007.04.033
9. W. C. Still, A. Tempczyk, R. C. Hawley, and T. Hendrickson, J. Am. Chem. Soc. 112, 6127 (1990). 10.1021/ja00172a038
10. D. Bashford and D. A. Case, Annu. Rev. Phys. Chem. 51, 129 (2000). 10.1146/annurev.physchem.51.1.129
11. M. S. Lee, F. R. Salsbury, and C. L. Brooks III, J. Chem. Phys. 116, 10606 (2002). 10.1063/1.1480013
12. J. Chen, C. L. Brooks III, and J. Khandogin, Curr. Opin. Struct. Biol. 18, 140 (2008).
13. T. Grycuk, J. Chem. Phys. 119, 4817 (2003). 10.1063/1.1595641
14. M. Feig and C. L. Brooks III, Curr. Opin. Struct. Biol. 14, 217 (2004). 10.1016/j.sbi.2004.03.009
15. C. J. Cramer and D. G. Truhlar, Chem. Rev. 99, 2161 (1999). 10.1021/cr960149m
16. B. Roux, Implicit Solvent Models, Computational Biochemistry, and Biophysics (Dekker, New York, 2001).
17. Z. Xu and W. Cai (unpublished).
18. A. H. Boschitsch, M. O. Fenley, and H. X. Zhou, J. Phys. Chem. B 106, 2741 (2002). 10.1021/jp013607q
19. B. Lu, X. Cheng, J. Huang, and J. A. McCammon, Proc. Natl. Acad. Sci. U.S.A. 103, 19314 (2006). 10.1073/pnas.0605166103
20. B. Z. Lu, Y. C. Zhou, M. J. Holst, and J. A. McCammon, Comm. Comp. Phys. 3, 973 (2008).
21. M. Baptista, R. Schmitz, and B. Dunweg, Phys. Rev. E 80, 016705 (2009). 10.1103/PhysRevE.80.016705
22. Y. Lin, A. Baumketner, S. Deng, Z. Xu, D. Jacobs, and W. Cai, J. Chem. Phys. 131, 154103 (2009). 10.1063/1.3245232
23. W. Cai, Z. Xu, and A. Baumketner, J. Comput. Phys. 227, 10162 (2008). 10.1016/j.jcp.2008.08.015
24. T. Schupbach, V. Zoete, B. Tsakam-Sotche, and O. Michielin, J. Comput. Chem. 31, 649 (2010).
25. Z. H. Duan and R. Krasny, J. Comput. Chem. 22, 184 (2001). 10.1002/1096-987X(20010130)22:2<184::AID-JCC6>3.0.CO;2-7
26. K. Lindsay and R. Krasny, J. Comput. Phys. 172, 879 (2001). 10.1006/jcph.2001.6862
27. P. Li, H. Johnston, and R. Krasny, J. Comput. Phys. 228, 3858 (2009). 10.1016/j.jcp.2009.02.022
28. W. H. Press, S. A. Teukolsky, W. T. Vetterling, and B. P. Flannery, Numerical Recipes in C: The Art of Scientific Computing (Cambridge University Press, New York, 1992).
29. J. Mongan, W. A. Svrcek-Seiler, and A. Onufriev, J. Chem. Phys. 127, 185101 (2007). 10.1063/1.2783847
30. H. Tjong and H.-X. Zhou, J. Phys. Chem. B 111, 3055 (2007). 10.1021/jp066284c
31. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaninathan, and M. Karplus, J. Comput. Chem. 4, 187 (1983). 10.1002/jcc.540040211