An iterative, fast, linear-scaling method for computing induced charges on arbitrary dielectric boundaries

Journal of Chemical Physics

Volumn 132, Issue 15, 2010, Pages

  Tyagi, Sandeep ^a   Süzen, Mehmet ^a   Sega, Marcello ^b   Barbosa, Marcia ^c   Kantorovich, Sofia S ^d   Holm, Christian ^d  

^a FRANKFURT INSTITUTE FOR ADVANCED STUDIES   (Germany)

^b UNIVERSITY OF TRENTO   (Italy)

^c FEDERAL UNIVERSITY OF RIO GRANDE DO SUL   (Brazil)

^d UNIVERSITY OF STUTTGART   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARBITRARY NUMBER; ARBITRARY SHAPE; COARSE GRAINED MODELS; COARSE-GRAINED MOLECULAR DYNAMICS SIMULATIONS; COMPUTATIONAL SPEED; DIELECTRIC BOUNDARY; DIELECTRIC DISCONTINUITY; DIELECTRIC PERMITTIVITIES; IMPLICIT SOLVENT MODEL; INDUCED CHARGES; LINEAR SCALING METHOD; PERIODIC BOUNDARY CONDITIONS; POLARIZATION EFFECT; SCALING BEHAVIOR; SOFT CONDENSED MATTERS;

MOLECULAR DYNAMICS;

THREE DIMENSIONAL;

ALGORITHM; ARTICLE; MOLECULAR DYNAMICS; STATIC ELECTRICITY;

ALGORITHMS; MOLECULAR DYNAMICS SIMULATION; STATIC ELECTRICITY;

EID: 77951687164     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3376011     Document Type: Article

References (52)

1. S. J. Marrink, A. H. de Vries, and A. E. Mark, J. Phys. Chem. B JPCBFK 1089-5647 108, 750 (2004). 10.1021/jp036508g
2. S. J. Marrink, H. J. Risselada, S. Yefimov, D. P. Tieleman, and A. H. de Vries, J. Phys. Chem. B JPCBFK 1089-5647 111, 7812 (2007). 10.1021/jp071097f (Pubitemid 47169693)
3. M. Brodholt, J. Sampoli, and R. Vallauri, Mol Phys. 85, 149 (1995). 10.1080/00268979500101901
4. G. Lamoureux, E. Harder, I. V. Vorobyov, B. Roux, and A. D. MacKerell, Jr., Chem. Phys. Lett. CHPLBC 0009-2614 418, 245 (2006). 10.1016/j.cplett.2005. 10.135 (Pubitemid 43063383)
5. T. A. Halgren and W. Damm, Curr. Opin. Struct. Biol. COSBEF 0959-440X 11, 236 (2001). 10.1016/S0959-440X(00)00196-2 (Pubitemid 32289428)
6. J. Warwicker and H. Watson, J. Mol. Biol. JMOBAK 0022-2836 157, 671 (1982). 10.1016/0022-2836(82)90505-8
7. M. Davis and J. McCammon, J. Comput. Chem. JCCHDD 0192-8651 12, 909 (1991). 10.1002/jcc.540120718
8. S. Chung, T. Allen, M. Hoyles, and S. Kuyucak, Biophys. J. BIOJAU 0006-3495 77, 2517 (1999). 10.1016/S0006-3495(99)77087-6
9. D. Levitt, Biophys. J. BIOJAU 0006-3495 22, 209 (1978). 10.1016/S0006-3495(78)85485-X
10. B. Honig, K. Sharp, and A. Yang, J. Phys. Chem. JPCHAX 0022-3654 97, 1101 (1993). 10.1021/j100108a002
11. B. Lu, X. Cheng, J. Huang, and J. A. McCammon, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 103, 19314 (2006). 10.1073/pnas.0605166103 (Pubitemid 46026029)
12. M. D. Altman, J. P. Bardhan, J. K. White, and B. Tidor, J. Comput. Chem. JCCHDD 0192-8651 30, 132 (2009). 10.1002/jcc.21027
13. T. Brumleve and R. Buck, J. Electroanal. Chem. JECHES 0022-0728 90, 1 (1978). 10.1016/S0022-0728(78)80137-5
14. D. Chen, J. Lear, and B. Eisenberg, Biophys. J. BIOJAU 0006-3495 72, 97 (1997). 10.1016/S0006-3495(97)78650-8
15. B. Corry, S. Kuyucak, and S. Chung, Biophys. J. BIOJAU 0006-3495 78, 2364 (2000). 10.1016/S0006-3495(00)76781-6
16. S. Rush, A. Turner, and A. Cherin, J. Appl. Phys. JAPIAU 0021-8979 37, 2211 (1966). 10.1063/1.1708789
17. S. Miertuš, E. Scrocco, and J. Tomasi, Chem. Phys. CMPHC2 0301-0104 55, 117 (1981). 10.1016/0301-0104(81)85090-2
18. P. B. Shaw, Phys. Rev. A PLRAAN 1050-2947 32, 2476 (1985). 10.1103/PhysRevA.32.2476
19. R. Bharadwaj, A. Windemuth, S. Sridharan, B. Honig, and A. Nicholls, J. Comput. Chem. JCCHDD 0192-8651 16, 898 (1995). 10.1002/jcc.540160707
20. J. Liang and S. Subramaniam, Biophys. J. BIOJAU 0006-3495 73, 1830 (1997). 10.1016/S0006-3495(97)78213-4
21. D. Chipman, J. Chem. Phys. JCPSA6 0021-9606 120, 5566 (2004). 10.1063/1.1648632
22. K. Sharp and B. Honig, Annu. Rev. Biophys. Biophys. Chem. ARBCEY 0883-9182 19, 301 (1990). 10.1146/annurev.bb.19.060190.001505
23. J. Tomasi and M. Persico, Chem. Rev. (Washington, D.C.) CHREAY 0009-2665 94, 2027 (1994). 10.1021/cr00031a013
24. C. Cramer and D. Truhlar, Chem. Rev. (Washington, D.C.) CHREAY 0009-2665 99, 2161 (1999). 10.1021/cr960149m
25. D. Boda, D. Gillespie, W. Nonner, D. Henderson, and B. Eisenberg, Phys. Rev. E PLEEE8 1063-651X 69, 046702 (2004). 10.1103/PhysRevE.69.046702
26. R. Allen, J. P. Hansen, and S. Melchionna, Phys. Chem. Chem. Phys. PPCPFQ 1463-9076 3, 4177 (2001). 10.1039/b105176h
27. J. Bardhan, J. Chem. Phys. JCPSA6 0021-9606 130, 094102 (2009). 10.1063/1.3080769
28. J. Bardhan, R. Eisenberg, and D. Gillespie, Phys. Rev. E PLEEE8 1063-651X 80, 011906 (2009). 10.1103/PhysRevE.80.011906
29. V. Rokhlin, J. Comput. Phys. JCTPAH 0021-9991 60, 187 (1985). 10.1016/0021-9991(85)90002-6
30. M. Fenley, W. Olson, K. Chua, and A. Boschitsch, J. Comput. Chem. JCCHDD 0192-8651 17, 976 (1996). 10.1002/(SICI)1096-987X(199606)17:8<976::AID- JCC7>3.0.CO;2-O
31. R. Zauhar and A. Varnek, J. Comput. Chem. JCCHDD 0192-8651 17, 864 (1996). 10.1002/(SICI)1096-987X(199605)17:7<864::AID-JCC10>3.0.CO;2-B
32. Y. Vorobjev and H. Scheraga, J. Comput. Chem. JCCHDD 0192-8651 18, 569 (1997). 10.1002/(SICI)1096-987X(199703)18:4<569::AID-JCC10>3.0.CO;2-B
33. E. Purisima, J. Comput. Chem. JCCHDD 0192-8651 19, 1494 (1998). 10.1002/(SICI)1096-987X(199810)19:13<1494::AID-JCC6>3.0.CO;2-L
34. A. Boschitsch, M. Fenley, and H. Zhous, J. Phys. Chem. B JPCBFK 1089-5647 106, 2741 (2002). 10.1021/jp013607q (Pubitemid 35275953)
35. A. Bordner and G. Huber, J. Comput. Chem. JCCHDD 0192-8651 24, 353 (2003). 10.1002/jcc.10195
36. F. Figueirido, R. Levy, R. Zhou, and B. Berne, J. Chem. Phys. JCPSA6 0021-9606 106, 9835 (1997). 10.1063/1.474115
37. E. Pollock and J. Glosli, Comput. Phys. Commun. CPHCBZ 0010-4655 95, 93 (1996). 10.1016/0010-4655(96)00043-4
38. J. D. Jackson, Classical Electrodynamics, 3rd ed. (Wiley, New York, 1999).
39. R. Zauhar and R. Morgan, J. Mol. Biol. JMOBAK 0022-2836 186, 815 (1985). 10.1016/0022-2836(85)90399-7
40. D. M. Young, Comput. Phys. Commun. CPHCBZ 0010-4655 53, 1 (1989). 10.1016/0010-4655(89)90145-8
41. L. Greengard and V. Rhoklin, J. Comput. Phys. JCTPAH 0021-9991 73, 325 (1987). 10.1016/0021-9991(87)90140-9
42. R. W. Hockney and J. W. Eastwood, Computer Simulations Using Particles (McGraw-Hill, New York, 1981).
43. M. Deserno and C. Holm, J. Chem. Phys. JCPSA6 0021-9606 109, 7678 (1998). 10.1063/1.477414 (Pubitemid 128678339)
44. M. Deserno and C. Holm, J. Chem. Phys. JCPSA6 0021-9606 109, 7694 (1998). 10.1063/1.477415 (Pubitemid 128678340)
45. A. Arnold, J. de Joannis, and C. Holm, J. Chem. Phys. JCPSA6 0021-9606 117, 2496 (2002). 10.1063/1.1491955 (Pubitemid 34945434)
46. A. Arnold and C. Holm, Comput. Phys. Commun. CPHCBZ 0010-4655 148, 327 (2002). 10.1016/S0010-4655(02)00586-6
47. A. Arnold and C. Holm, J. Chem. Phys. JCPSA6 0021-9606 123, 144103 (2005). 10.1063/1.2052647 (Pubitemid 41476699)
48. A. Bródka, J. Chem. Phys. JCPSA6 0021-9606 125, 107103 (2006). 10.1063/1.2346457
49. S. Tyagi, A. Arnold, and C. Holm, J. Chem. Phys. JCPSA6 0021-9606 127, 154723 (2007). 10.1063/1.2790428 (Pubitemid 351260812)
50. S. Tyagi, A. Arnold, and C. Holm, J. Chem. Phys. JCPSA6 0021-9606 129, 204102 (2008). 10.1063/1.3021064
51. H. J. Limbach, A. Arnold, B. A. Mann, and C. Holm, Comput. Phys. Commun. CPHCBZ 0010-4655 174, 704 (2006). 10.1016/j.cpc.2005.10.005
52. S. Cui and H. Cochran, J. Chem. Phys. JCPSA6 0021-9606 117, 5850 (2002). 10.1063/1.1501585 (Pubitemid 35170686)