GPU accelerated implementation of density functional theory for hybrid QM/MM simulations

Journal of Chemical Theory and Computation

Volumn 10, Issue 3, 2014, Pages 959-967

  Nitsche, Matías A ^a   Ferreria, Manuel ^b   Mocskos, Esteban E ^a,b   Lebrero, Mariano C González ^b  

^a UNIVERSIDAD DE BUENOS AIRES   (Argentina)

^b Centro de Simulación Computacional Para Aplicaciones Tecnológicas CSC CONICET ^*  (Argentina)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84896276143     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct400308n     Document Type: Article

References (32)

1. Yasuda, K. J. Comput. Chem. 2008, 29, 334-342
2. Vogt, L.; Olivares-Amaya, R.; Kermes, S.; Shao, Y.; Amador-Bedolla, C.; Aspuru-Guzik, A. J. Phys. Chem. A 2008, 112, 2049-2057
3. Ufimtsev, I. S.; Martinez, T. J. J. Chem. Theory Comput. 2008, 4, 222-231
4. Genovese, L.; Ospici, M.; Deutsch, T.; Méhaut, J.; Neelov, A.; Goedecker, S. J. Chem. Phys. 2009, 131, 034103
5. Stone, J. E.; Phillips, J. C.; Freddolino, P. L.; Hardy, D. J.; Trabuco, L. G.; Schulten, K. J. Comput. Chem. 2007, 28, 2618-2640
6. Anderson, A. G.; W. A., G., III; Schröder, P. Comput. Phys. Commun. 2007, 177, 298-306
7. Wilkinson, K.; Skylaris, C.-K. J. Comput. Chem. 2013, 34, 2446-2459
8. TeraChem v1.0. http://www.petachem.com (accessed February 17, 2014).
9. Yasuda, K. J. Chem. Theory Comput. 2008, 4, 1230-1236
10. Capece, L.; Marti, M.; Crespo, A.; Doctorovich, F.; Estrin, D. J. Am. Chem. Soc. 2006, 128, 12455-12461
11. Crespo, A.; Scherlis, D.; Martí, M.; Ordejón, P.; Roitberg, A.; Estrin, D. J. Phys. Chem. B 2003, 107, 13728-13736
12. Crespo, A.; Martí, M.; Estrin, D.; Roitberg, A. J. Am. Chem. Soc. 2005, 127, 6940-6941
13. Crespo, A.; Marti, M.; Kalko, S.; Morreale, A.; Orozco, M.; Gelpi, J.; Luque, F.; Estrin, D. J. Am. Chem. Soc. 2005, 127, 4433-4444
14. Friesner, R.; Guallar, V. Annu. Rev. Phys. Chem. 2005, 56, 389-427
15. Marti, M.; Crespo, A.; Bari, S.; Doctorovich, F.; Estrin, D. J. Phys. Chem. B 2004, 108, 18073-18080
16. Ridder, L.; Harvey, J.; Rietjens, I.; Vervoort, J.; Mulholland, A. J. Phys. Chem. B 2003, 107, 2118-2126
17. Sproviero, E.; Gascón, J.; McEvoy, J.; Brudvig, G.; Batista, V. J. Chem. Theory Comput. 2006, 2, 1119-1134
18. Estrin, D.; Corongiu, G.; Clementi, E. In Methods and Techniques in Computational Chemistry; Clementi, E., Ed.; STEF: Cagliari, Italy, 1993; Chapter 12.
19. Yasuda, K. J Chem. Theory Comput. 2008, 4, 1230-1236
20. Case, D. AMBER 12; University of California, San Francisco: San Francisco, CA, 2012.
21. Kohn, W.; Sham, L. J. Phys. Rev. 1965, 140, A1133-A1138
22. Becke, A. D. J. Chem. Phys. 1988, 88, 2547-2553
23. Stratmann, R.; Scuseria, G. E.; Frisch, M. J. Chem. Phys. Lett. 1996, 257, 213-223
24. Götz, A. W.; Clark, M. A.; Walker, R. C. J. Comput. Chem. 2014, 35, 95-108
25. Zeida, A.; Lebrero, M. C. G.; Radi, R.; Trujillo, M.; Estrin, D. A. Arch. Biochem. Biophys. 2013, 539, 81-86
26. TeraChem Performance Analysis. http://www.petachem.com/performance.html (accessed February 17, 2014).
27. Perdew, J. P.; Burke, K.; Ernzerhof, M. Phys. Rev. Lett. 1996, 77, 3865-3868
28. Lebedev, V. I. USSR Comput. Math. Math. Phys. 1975, 15, 44-51
29. Lebedev, V. I. USSR Comput. Math. Math. Phys. 1976, 16, 10-24
30. The NVIDIA CUDA Basic Linear Algebra Subroutines. https://developer. nvidia.com/cuBLAS (accessed February 17, 2014).
31. CUDA Toolkit 5.0 Performance Report. https://developer.nvidia.com/sites/ default/files/akamai/cuda/files/CUDACUDA-5.0 Math-Libraries- Performance.pdf (accessed February 17, 2014).
32. Tsuda, T.; Toyoshima, C. EMBO J. 2009, 1782-1791