Molecular dynamics simulations on commodity GPUs with CUDA

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 4873 LNCS, Issue , 2007, Pages 185-196

  Liu, Weiguo ^a   Schmidt, Bertil ^b   Voss, Gerrit ^a   Müller Wittig, Wolfgang ^a  

^a NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

^b UNIVERSITY OF NEW SOUTH WALES   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ATOMS; COMPUTER SIMULATION; GRAPHIC METHODS; MOLECULAR BIOLOGY; PARALLEL ALGORITHMS; SOFTWARE ARCHITECTURE;

COMPUTE UNIFIED DEVICE ARCHITECTURE (CUDA); GRAPHICS PROCESSING UNITS; MOLECULAR DYNAMICS SIMULATIONS; PROGRAMMABILITY;

MOLECULAR DYNAMICS;

EID: 38349105400     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-77220-0_20     Document Type: Conference Paper

References (23)

1. Krüger, J., Westermann, R.: Linear algebra operators for gpu implementation of numerical algorithms. ACM Trans. Graph. 22, 908-916 (2003)
2. Xu, F., Müller, K.: Ultra-fast 3d filtered backprojection on commodity graphics hardware. In: IEEE International Symposium on Biomedical Imaging 2004 (2004)
3. Liu, W., Schmidt, B., Voss, G., Müller-Wittig, W.: Streaming algorithms for biological sequence alignment on gpus. IEEE Transactions on Parallel and Distributed Systems 18(9), 1270-1281 (2007)
4. Horn, D., Houston, M., Hanrahan, P.: Clawhmmer: a streaming hmmer-search implementation. In: Proceedings of Supercomputing 2005 (2005)
5. Moreland, K., Angel, E.: The fft on a gpu. In: Proceedings SIGGRAPH/Eurographics Workshop on Graphics Hardware, pp. 112-119 (2003)
6. Owens, J., Luebke, D., Govindaraju, N., Harris, M., Kruger, J., Lefohn, A., Purcell, T.: A survey of general-purpose computation on graphics hardware. In: Eurographics 2005, pp. 21-51 (2005)
7. Nvidia: NVIDIA CUDA Homepage, http://developer.nvidia.com/object/cuda. html
8. Sheng, H., Guerrieri, R., Sangiovanni-Vincentelli, A.L.: Three-dimensional monte carlo device simulation for massively parallel architectures. Technical Report UCB/ERL M95/53, EECS Department, University of California, Berkeley (1995)
9. Ercolessi, F.: A molecular dynamics primer. Technical report (1997) http://www.fisica.uniud.it/~ercolessi/md/
10. Allen, M.: Introduction to molecular dynamics simulation. Computational Soft Matter-From Synthetic Polymers to Proteins 23, 1-28 (2004)
11. Lennard-Jones, J.: Cohesion. In: Proceedings of Physical Society, pp. 461-482 (1931)
12. Shu, J., Wang, B., Zheng, W.: Cluster-based parallel simulation for large scale molecular dynamics in microscale thermophysics. In: Cao, J., Yang, L.T., Guo, M., Lau, F. (eds.) ISPA 2004. LNCS, vol. 3358, pp. 200-211. Springer, Heidelberg (2004)
13. Plimpton, S.: Fast parallel algorithms for short-range molecular dynamics. Journal of Computational Physics 117, 1-19 (1995)
14. Hut, P., Makino, J.: Computational physics - astrophysics on the grape family of special-purpose computers. Science 283, 501-505 (1999)
15. Bakker, A., Gilmer, G., Grabow, M., Thompson, K.: A special purpose computer for molecular dynamics calculations. Journal of Computational Physics 90, 313-335 (1990)
16. Fine, R., Dimmler, G., Levinthal, C.: Fastrun: A special purpose, hardwired computer for molecular simulation. Proteins 11, 242-253 (1991)
17. Narumi, T., Ohno, Y., Okimoto, N., Suenaga, A., Yanai, R., Taiji, M.: A high-speed special-purpose computer for molecular dynamics simulations: Mdgrape-3. In: NIC Workshop 2006, vol. 34, pp. 29-36 (2006)
18. Mink, A., Bailly, C.: Parallel implementation of a molecular dynamics simulation program. In: Simulation Conference Proceedings, vol. 1, pp. 13-16 (1998)
19. Nakano, P., Kalia, R.: Parallel multiple-time-step molecular dynamics with three-body interaction. Computer Physics Communications 77, 303-312 (1993)
20. Tamayo, P., Mesirov, J., Boghosian, B.: Parallel approaches to short-range molecular dynamics simulations. Supercomputing, 462-470 (1991)
21. Nvidia: NVIDIA CUDA Compute Unified Device Architecture-Programming Guide, (2007) http://developer.download.nvidia.com/compute/cuda
22. Berendsen, H., Van Der Spoel, D., Van Drunen, R.: Gromacs: A message-passing parallel molecular dynamics implementation. Computer Physics Communications 91, 43-56 (1995)
23. Morris, G., Goodsell, D., Huey, R., Olson, A.: Distributed automated docking of flexible ligands to proteins: Parallel applications of autodock 2.4. Journal of Computer-Aided Molecular Design 10(2), 293-304 (1996)