Accelerating Molecular Dynamics Simulation Using Graphics Processing Unit
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Myung, Hun-Joo
(KISTI Supercomputing Center)
Sakamaki, Ryuji (Department of Mechanical Engineering, Keio University) Oh, Kwang-Jin (KISTI Supercomputing Center) Narumi, Tetsu (Department of Computer Science, University of Electro-Communications) Yasuoka, Kenji (Department of Mechanical Engineering, Keio University) Lee, Sik (KISTI Supercomputing Center) |
1 | Ryckaert, J.-P.; Ciccotti, G.; Berendsen, H. J. C. J. Comp. Phys. 1977, 23, 327. DOI ScienceOn |
2 | Andersen, H. C. J. Comp. Phys. 1983, 52, 24. DOI ScienceOn |
3 | Narumi, T.; Kameoka, S.; Taiji, M.; Yasuoka, K. SIAM J. Sci. Comp. 2008, 30, 3108. DOI ScienceOn |
4 | Narumi, T.; Hamada, T.; Nitadori, K.; Sakamaki, R.; Kameoka, S.; Yasuoka, K. High-Performance Quasi Double-Precision Method using Single-Precision Hardware for Molecular Dynamics Simulations with GPUs; 10th International Conference on High Performance Computing in Asia-Pacific Region, 2009. |
5 | Anderson, J. A.; Lorenz, C. D.; Travesset, A. J. Comp. Phys. 2008, 227, 5342. DOI ScienceOn |
6 | Stone, J. E.; Phillips, J. C.; Freddolino, P. L.; Hardy, D. J.; Trabuco, L. G.; Schulten, K. J. Comp. Chem. 2007, 28, 2618. DOI ScienceOn |
7 | Yang, J.; Wang, Y.; Chen, Y. J. Comp. Phys. 2007, 221, 799. DOI ScienceOn |
8 | van Meel, J. A.; Arnold, A.; Frenkel, D.; Portegies Zwart, S. F.; Belleman, R. G. Mol. Sim. 2008, 34, 259. DOI ScienceOn |
9 | Hardy, D. J.; Stone, J. E.; Schulten, K. Parallel Computing 2009, 35, 164. DOI ScienceOn |
10 | Liu, W.; Schmidt, B.; Voss, G.; Muller-Wittig, W. Comp. Phys. Comm. 2008, 179, 634. DOI ScienceOn |
11 | Taufer, M.; Saponaro, P.; Padron, O.; Patel, S. Improving Numerical Reproducibility and Stability in Large-Scale Numerical Simulations on GPUs; 24th IEEE International Parallel and Distributed Processing Symposium, 2009. |
12 | Friedrichs, M. S.; Eastman, P.; Vaidyanathan, V.; Houston, M.; Legrand, S.; Beberg, A. L.; Ensign, D. L.; Bruns, C. M.; Pande, V. S. J. Comp. Chem. 2009, 30, 864. DOI ScienceOn |
13 | MacKerell, A., Jr.; Bashford, D.; Bellott, M.; Dunbrack, R. L., Jr.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher W. E., III.; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J. Phys. Chem. B 1998, 102, 3586. DOI ScienceOn |
14 | Oh, K. J.; Klen, M. L. Comp. Phys. Comm. 2006, 174, 560. DOI ScienceOn |
15 | http://www.nvidia.com. |
16 | Smith, W. Comp. Phys. Comm. 1991, 62, 229. DOI ScienceOn |
17 | Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926. DOI |
18 | Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids; Clarendon: Oxford, 1987. |
19 | Smit, B.; Frenkel, D. Understanding Molecular Simulation; Academic Press: Orlando, 2001. |
20 | Shelley, J. C.; Shelley, M. Y.; Reeder, R. C.; Bandyopadhyay, S.; Klein, M. L. J. Phys. Chem. B 2001, 105, 4464. DOI ScienceOn |
21 | Plimpton, S. J. Comp. Phys. 1995, 117, 1. DOI ScienceOn |
22 | Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. J. Chem. Phys. 1995, 103, 8577. DOI ScienceOn |
23 | Martyna, G. J.; Tuckerman, M. E.; Tobias, D. J.; Klein, M. L. Mol. Phys. 1996, 87, 1117. DOI ScienceOn |
24 | Minary, P.; Tuckerman, M. E.; Martyna, G. J. Phys. Rev. Lett. 2004, 93, 150201. DOI ScienceOn |
25 | Oh, K. J.; Deng, Y. Comp. Phys. Comm. 2007, 177, 426. DOI ScienceOn |
26 | Oh, K. J.; Klein, M. L. Comp. Phys. Comm. 2006, 174, 263. DOI ScienceOn |
27 | Moore, G. E. Electronics Magazine 1965, 38, 4. |
28 | http://www.top500.org. |
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