An improved isotropic periodic sum method that uses linear combinations of basis potentials

Journal of Chemical Theory and Computation

Volumn 8, Issue 11, 2012, Pages 4503-4516

  Takahashi, Kazuaki Z ^a   Narumi, Tetsu ^b   Suh, Donguk ^a   Yasuoka, Kenji ^a  

^a KEIO UNIVERSITY   (Japan)

^b UNIVERSITY OF ELECTRO COMMUNICATIONS   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84869054114     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct3003805     Document Type: Article

References (67)

1. Hoheisel, C. J. Chem. Phys. 1987, 86, 2328
2. Hoheisel, C.; Vogelsang, R.; Schoen, M. J. Chem. Phys. 1987, 87, 7195
3. Smit, B. J. Chem. Phys. 1992, 96, 8639-8640
4. Trokhymchuk, A.; Alejandre, J. J. Chem. Phys. 1999, 111, 8510
5. Lopez-Lemus, J.; Alejandre, J. Mol. Phys. 2002, 100, 2983-2992
6. Neumann, M.; Steinhauser, O. Mol. Phys. 1980, 39, 437-454
7. Alper, H.; Levy, R. J. Chem. Phys. 1989, 91, 1242
8. Kitchen, D.; Hirata, F.; Westbrook, J.; Levy, R.; Kofke, D.; Yarmush, M. J. Comput. Chem. 1990, 11, 1169-1180
9. Tasaki, K.; McDonald, S.; Brady, J. J. Comput. Chem. 1993, 14, 278-284
10. Smith, P.; van Gunsteren, W. J. Chem. Phys. 1994, 100, 3169
11. Feller, S.; Pastor, R.; Rojnuckarin, A.; Bogusz, S.; Brooks, B. J. Phys. Chem. 1996, 100, 17011-17020
12. van der Spoel, D.; van Maaren, P.; Berendsen, H. J. Chem. Phys. 1998, 108, 10220
13. Mark, P.; Nilsson, L. J. Comput. Chem. 2002, 23, 1211-1219
14. Yonetani, Y. Chem. Phys. Lett. 2005, 406, 49-53
15. van der Spoel, D.; van Maaren, P. J. Chem. Theory Comput. 2006, 2, 1-11
16. Yonetani, Y. J. Chem. Phys. 2006, 124 204501
17. Mathias, G.; Egwolf, B.; Nonella, M.; Tavan, P. J. Chem. Phys. 2003, 118, 10847
18. Mathias, G.; Tavan, P. J. Chem. Phys. 2004, 120, 4393
19. Lorenzen, K.; Schwörer, M.; Tröster, P.; Mates, S.; Tavan, P. J. Chem. Theory Comput. 2012, not supplied.
20. Loncharich, R.; Brooks, B. Proteins: Struct., Funct., Bioinf. 1989, 6, 32-45
21. Schreiber, H.; Steinhauser, O. Biochemistry 1992, 31, 5856-5860
22. Schreiber, H.; Steinhauser, O. Chem. Phys. 1992, 168, 75-89
23. Schreiber, H.; Steinhauser, O. J. Mol. Biol. 1992, 228, 909-923
24. Saito, M. Mol. Simul. 1992, 8, 321-333
25. Guenot, J.; Kollman, P. Journal of computational chemistry 1993, 14, 295-311
26. Saito, M. J. Chem. Phys. 1994, 101, 4055
27. Oda, K.; Miyagawa, H.; Kitamura, K. Mol. Simul. 1996, 16, 167-177
28. Norberg, J.; Nilsson, L. Biophys. J. 2000, 79, 1537-1553
29. Patra, M.; Karttunen, M.; Hyvönen, M.; Falck, E.; Lindqvist, P.; Vattulainen, I. Biophys. J. 2003, 84, 3636-3645
30. Beck, D.; Armen, R.; Daggett, V. Biochemistry 2005, 44, 609-616
31. Monticelli, L.; Simões, C.; Belvisi, L.; Colombo, G. J. Phys.: Condens. Matter 2006, 18, S329
32. Reif, M.; Kräutler, V.; Kastenholz, M.; Daura, X.; Hünenberger, P. J. Phys. Chem. B 2009, 113, 3112-3128
33. Ewald, P. Ann. Phys 1921, 64, 253-287
34. Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98, 10089
35. Essmann, U.; Perera, L.; Berkowitz, M.; Darden, T.; Lee, H.; Pedersen, L. J. Chem. Phys. 1995, 103, 8577-8593
36. Frenkel, D.; Smit, B. Understanding molecular simulation: from algorithms to applications; Academic Press: San Diego, CA, 2002; Vol. 1.
37. Kia, A.; Kim, D.; Darve, E. J. Comput. Phys. 2008, 227, 8551-8567
38. Yokota, R.; Narumi, T.; Barba, L.; Yasuoka, K. Arxiv preprint 2011, arXiv:1106.5273
39. Andoh, Y.; Okazaki, S. Private communication, 2012.
40. Barnes, J.; Hut, P. Nature 1986, 324, 4
41. Greengard, L.; Rokhlin, V. J. Comput. Phys. 1987, 73, 325-348
42. Zhou, R.; Berne, B. J. Chem. Phys. 1995, 103, 9444
43. Petersen, H. J. Chem. Phys. 1995, 103, 3668
44. Pollock, E.; Glosli, J. Comput. Phys. Commun. 1996, 95, 93-110
45. Lim, K.; Brunett, S.; Iotov, M.; McClurg, R.; Vaidehi, N.; Dasgupta, S.; Taylor, S.; Goddard, W., III. J. Comput. Chem. 1997, 18, 501-521
46. Figueirido, F.; Levy, R.; Zhou, R.; Berne, B. J. Chem. Phys. 1997, 106, 9835-9849
47. Dimitrov, D.; Raev, N. J. Electroanal. Chem. 2000, 486, 1-8
48. Wang, Z.; Lupo, J.; Patnaik, S.; Pachter, R. Comput. Theor. Polym. Sci. 2001, 11, 375-387
49. Deng, S.; Cai, W. J. Comput. Phys. 2007, 227, 1246-1266
50. Wu, X.; Brooks, B. J. Chem. Phys. 2005, 122 044107
51. Wu, X.; Brooks, B. J. Chem. Phys. 2008, 129 154115
52. Wu, X.; Brooks, B. J. Chem. Phys. 2009, 131 024107
53. Takahashi, K.; Yasuoka, K.; Narumi, T. J. Chem. Phys. 2007, 127 114511
54. Takahashi, K.; Narumi, T.; Yasuoka, K. J. Chem. Phys. 2010, 133 014109
55. Takahashi, K.; Narumi, T.; Yasuoka, K. Mol. Simul. 2012, 38, 397-403
56. Klauda, J.; Wu, X.; Pastor, R.; Brooks, B. J. Phys. Chem. B 2007, 111, 4393-4400
57. Takahashi, K.; Narumi, T.; Yasuoka, K. J. Chem. Phys. 2011, 134 174112
58. Venable, R.; Chen, L.; Pastor, R. J. Phys. Chem. B 2009, 113, 5855-5862
59. Takahashi, K.; Narumi, T.; Yasuoka, K. J. Chem. Phys. 2011, 135 174108
60. Narumi, T.; Ohno, Y.; Okimoto, N.; Koishi, T.; Suenaga, A.; Futatsugi, N.; Yanai, R.; Himeno, R.; Fujikawa, S.; Ikei, M.; Taiji, M. A 55 TFLOPS Simulation of Amyloid forming Peptides from Yeast Prion Sup35 with the Specialpurpose Computer System MDGRAPE-3, 2006.
61. Taiji, M. MDGRAPE-3 Chip: a 165-Gflops Application-Specific LSI for Molecular Dynamics Simulations, 2004.
62. Taiji, M.; Narumi, T.; Ohno, Y.; Futatsugi, N.; Suenaga, A.; Takada, N.; Konagaya, A. A Petaflops Special-Purpose Computer System for Molecular Dynamics Simulations, 2003.
63. Berendsen, H.; Grigera, J.; Straatsma, T. J. Phys. Chem. 1987, 91, 6269-6271
64. Swope, W.; Andersen, H.; Berens, P.; Wilson, K. J. Chem. Phys. 1982, 76, 637
65. Andersen, H. J. Comput. Phys. 1983, 52, 24-34
66. Nosé, S. J. Chem. Phys. 1984, 81, 511
67. Hoover, W. Phys. Rev. A 1985, 31, 1695