Modified anderson method for accelerating 3D-RISM calculations using graphics processing unit

Journal of Chemical Theory and Computation

Volumn 8, Issue 9, 2012, Pages 3015-3021

  Maruyama, Yutaka ^a   Hirata, Fumio ^a,b  

^a INSTITUTE FOR MOLECULAR SCIENCE   (Japan)

^b GRADUATE UNIVERSITY FOR ADVANCED STUDIES   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84866183329     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct300355r     Document Type: Article

References (77)

1. Hirata, F., Sato, H., Kinoshita, M., Kovalenko, A., and Chong, S.-H. Molecular Theory of Solvation; Hirata, F., Ed.; Kluwer Academic Publishers: Dordrecht, The Netherlands, 2003.
2. Imai, T.; Hiraoka, R.; Kovalenko, A.; Hirata, F. J. Am. Chem. Soc. 2005, 127, 15334
3. Imai, T.; Hiraoka, R.; Kovalenko, A.; Hirata, F. Proteins 2007, 66, 804
4. Yoshida, N.; Phongphanphanee, S.; Maruyama, Y.; Imai, T.; Hirata, F. J. Am. Chem. Soc. 2006, 128, 12042
5. Yoshida, N.; Phongphanphanee, S.; Hirata, F. J. Phys. Chem. B 2007, 111, 4588
6. Ikuta, Y.; Maruyama, Y.; Matsugami, M.; Hirata, F. Chem. Phys. Lett. 2007, 433, 403
7. Maruyama, Y.; Matsugami, M.; Ikuta, Y. Condens. Matter Phys. 2007, 10, 315
8. Phongphanphanee, S.; Yoshida, N.; Hirata, F. Chem. Phys. Lett. 2007, 449, 433
9. Phongphanphanee, S.; Yoshida, N.; Hirata, F. J. Am. Chem. Soc. 2008, 130, 1540
10. Phongphanphanee, S.; Yoshida, N.; Hirata, F. J. Mol. Liq. 2009, 147, 107
11. Yonetani, Y.; Maruyama, Y.; Hirata, F.; Kono, H. J. Chem. Phys. 2008, 128, 185102
12. Maruyama, Y.; Yoshida, N.; Hirata, F. J. Phys. Chem. B 2010, 114, 6464
13. Maruyama, Y.; Matsushita, T.; Ueoka, R.; Hirata, F. J. Phys. Chem. B 2011, 115, 2408
14. Miyata, T.; Hirata, F. J. Comput. Chem. 2008, 29, 871
15. Miyata, T.; Ikuta, Y.; Hirata, F. J. Chem. Phys. 2010, 133, 044114
16. Luchko, T.; Gusarov, S.; Roe, D. R.; Simmerling, C.; Case, D. A.; Tuszynski, J.; Kovalenko, A. J. Chem. Theory Comput. 2010, 6, 607
17. Genheden, S.; Luchko, T.; Gusarov, S.; Kovalenko, A.; Ryde, U. J. Phys. Chem. B 2010, 114, 8505
18. Kovalenko, A.; Hirata, F. J. Chem. Phys. 1999, 110, 10095
19. Sato, H.; Kovalenko, A.; Hirata, F. J. Comput. Chem. 2000, 112, 9463
20. Kovalenko, A.; Hirata, F. J. Mol. Liq. 2001, 90, 215
21. Yoshida, N.; Hirata, F. J. Comput. Chem. 2006, 27, 453
22. Gusarov, S.; Ziegler, T.; Kovalenko, A. J. Phys. Chem. A 2006, 110, 6083
23. Casanova, D.; Gusarov, S.; Kovalenko, A.; Ziegler, T. J. Chem. Theory Comput. 2007, 3, 458
24. Malvaldi, M.; Bruzzone, S.; Chiappe, C.; Gusarov, S.; Kovalenko, A. J. Phys. Chem. B 2009, 113, 3536
25. Li, Q. B.; Gusarov, S.; Evoy, S.; Kovalenko, A. J. Phys. Chem. B 2009, 113, 9958
26. Stone, J. E.; Phillips, J. C.; Freddolino, P. L.; Hardy, D. J.; Trabuco, L. G.; Schulten, K. J. Comput. Chem. 2007, 28, 2618
27. Yang, J. K.; Wang, Y. J.; Chen, Y. F. J. Comput. Phys. 2007, 221, 799
28. Anderson, J. A.; Lorenz, C. D.; Travesset, A. J. Comput. Phys. 2008, 227, 5342
29. van Meel, J. A.; Arnold, A.; Frenkel, D.; Zwart, S. F. P.; Belleman, R. G. Mol. Simul. 2008, 34, 259
30. Liu, W. G.; Schmidt, B.; Voss, G.; Muller-Wittig, W. Comput. Phys. Commun. 2008, 179, 634
31. Harvey, M. J.; Giupponi, G.; De Fabritiis, G. J. Chem. Theory Comput. 2009, 5, 1632
32. Chen, F. G.; Ge, W.; Li, J. H. Sci. China, Ser. B: Chem. 2009, 52, 372
33. Friedrichs, M. S.; Eastman, P.; Vaidyanathan, V.; Houston, M.; Legrand, S.; Beberg, A. L.; Ensign, D. L.; Bruns, C. M.; Pande, V. S. J. Comput. Chem. 2009, 30, 864
34. Hardy, D. J.; Stone, J. E.; Schulten, K. Parallel Comput. 2009, 35, 164
35. Narumi, T.; Yasuoka, K.; Taiji, M.; Hofinger, S. J. Comput. Chem. 2009, 30, 2351
36. Harvey, M. J.; De Fabritiis, G. J. Chem. Theory Comput. 2009, 5, 2371
37. Eastman, P.; Pande, V. S. J. Comput. Chem. 2010, 31, 1268
38. Cickovski, T.; Chatterjee, S.; Wenger, J.; Sweet, C. R.; Izaguirre, J. A. J. Comput. Chem. 2010, 31, 1345
39. Schmid, N.; Botschi, M.; Van Gunsteren, W. F. J. Comput. Chem. 2010, 31, 1636
40. Bauer, B. A.; Davis, J. E.; Taufer, M.; Patel, S. J. Comput. Chem. 2010, 32, 375
41. Sunarso, A.; Tsuji, T.; Chono, S. J. Comput. Phys. 2010, 229, 5486
42. Jha, P. K.; Sknepnek, R.; Guerrero-Garcia, G. I.; de la Cruz, M. O. J. Chem. Theory Comput. 2010, 6, 3058
43. Zhmurov, A.; Dima, R. I.; Kholodov, Y.; Barsegov, V. Proteins 2010, 78, 2984
44. Yasuda, K. J. Comput. Chem. 2008, 29, 334
45. Yasuda, K. J. Chem. Theory Comput. 2008, 4, 1230
46. Vogt, L.; Olivares-Amaya, R.; Kermes, S.; Shao, Y.; Amador-Bedolla, C.; Aspuru-Guzik, A. J. Phys. Chem. A 2008, 112, 2049
47. Ufimtsev, I. S.; Martinez, T. J. J. Chem. Theory Comput. 2008, 4, 222
48. Ufimtsev, I. S.; Martinez, T. J. J. Chem. Theory Comput. 2009, 5, 1004
49. Ufimtsev, I. S.; Martinez, T. J. J. Chem. Theory Comput. 2009, 5, 2619
50. Luehr, N.; Ufimtsev, I. S.; Martnez, T. J. J. Chem. Theory Comput. 2011, 7, 949
51. Isborn, C. M.; Luehr, N.; Ufimtsev, I. S.; Martnez, T. J. J. Chem. Theory Comput. 2011, 7, 1814
52. Genovese, L.; Ospici, M.; Deutsch, T.; Mehaut, J. F.; Neelov, A.; Goedecker, S. J. Comput. Phys. 2009, 131, 034103
53. Olivares-Amaya, R.; Watson, M. A.; Edgar, R. G.; Vogt, L.; Shao, Y. H.; Aspuru-Guzik, A. J. Chem. Theory Comput. 2010, 6, 135
54. Asadchev, A.; Allada, V.; Felder, J.; Bode, B. M.; Gordon, M. S.; Windus, T. L. J. Phys. Chem. 2010, 6, 696
55. Vysotskiy, V. P.; Cederbaum, L. S. J. Chem. Theory Comput. 2011, 7, 320
56. DePrince, A. E., III; Hammond, J. R. J. Chem. Theory Comput. 2011, 7, 1287
57. Ma, W.; Krishnamoorthy, S.; Villa, O.; Kowalski, K. J. Chem. Theory Comput. 2011, 7, 1316
58. Janes, P. P.; Rendell, A. P. J. Chem. Theory Comput. 2011, 7, 1631
59. Uejima, Y.; Terashima, T.; Maezono, R. J. Comput. Chem. 2011, 32, 2264
60. Wilkinson, K. A.; Sherwood, P.; Guest, M. F.; Naidoo, K. J. J. Comput. Chem. 2011, 32, 2313
61. Tesla C1060 GPU computing processor. http://www.nvidia.com/docs/IO/43395/ NV-DS-Tesla-C1060-US-Jan10-lores-r1.pdf (accessed June 6, 2012).
62. Tesla C2050/C2070 GPU computing processor. http://www.nvidia.com/docs/IO/ 43395/NV-DS-Tesla-C2050-C2070-jul10-lores.pdf (accessed June 6, 2012).
63. Intel Corporation, Intel QuickPath Architecture, White Paper. http://www.intel.com/content/dam/doc/white-paper/performance-quickpath- architecture-paper.pdf (accessed June 6, 2012).
64. Kovalenko, A.; Ten-No, S.; Hirata, F. J. Comput. Chem. 1999, 20, 928
65. Ooura, T. General Purpose FFT (Fast Fourier/Cosine/Sine Transform) Package. http://www.kurims.kyoto-u.ac.jp/1/4ooura/fft.html (accessed June 13, 2012).
66. Anderson, D. J. Assoc. Comput. Mach. 1965, 12, 547
67. Kovalenko, A.; Hirata, F. J. Phys. Chem. B. 1999, 103, 7942
68. Kovalenko, A.; Hirata, F. J. Chem. Phys. 1999, 110, 10095
69. Kovalenko, A.; Hirata, F. J. Chem. Phys. 2000, 112, 10391
70. Singer, S. J.; Chandler, D. Mol. Phys. 1985, 55, 621
71. Kovalenko, A.; Hirata, F. J. Chem. Phys. 1999, 110, 10095
72. Inaba, T.; Sato, F. J. Comput. Chem. 2007, 28, 984
73. Cieplak, P.; Caldwell, J.; Kollman, P. J. Comput. Chem. 2001, 22, 1048
74. Berendsen, H. J. C.; Grigera, J. R.; Straatsma, T. P. J. Chem. Phys. 1987, 91, 6269
75. Pettitt, B. M.; Rossky, P. J. J. Chem. Phys. 1982, 77, 1451
76. Nukada, A.; Ogata, Y.; Endo, T.; Matsuoka, S. Bandwidth Intensive 3-D FFT kernel for GPUs using CUDA. In Proceedings of the 2008 ACM/IEEE conference on Supercomputing, Austin, TX, November 15-21, 2008; Teller, P. J., Ed.; IEEE Press: Piscataway, NJ, 2008.
77. Nukada, A.; Matsuoka, S. Auto-Tuning 3-D FFT Library for CUDA GPUs. In Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis, Portland, OR, November 14-20, 2009; Pinfold, W., Ed.; ACM New York: New York, 2009.