Extending the generality of molecular dynamics simulations on a special-purpose machine

Proceedings - IEEE 27th International Parallel and Distributed Processing Symposium, IPDPS 2013

Volumn , Issue , 2013, Pages 933-945

  Scarpazza, Daniele P ^a   Ierardi, Douglas J ^a   Lerer, Adam K ^a   Mackenzie, Kenneth M ^a   Pan, Albert C ^a   Bank, Joseph A ^a   Chow, Edmond ^a,b   Dror, Ron O ^a   Grossman, J P ^a   Killebrew, Daniel ^a   Moraes, Mark A ^a   Predescu, Cristian ^a   Salmon, John K ^a   Shaw, David E ^a,c  

^a D E SHAW RESEARCH   (United States)

^b Georgia Institute of Technology   (United States)

^c Och Spine at New York Presbyterian Hospitals   (United States)

Author keywords

none

Indexed keywords

BIOLOGICAL PHENOMENA; GENERAL PURPOSE PROCESSORS; HARDWARE AND SOFTWARE DESIGNS; HETEROGENEOUS PARALLEL COMPUTING; MASSIVELY PARALLELS; MOLECULAR DYNAMICS SIMULATIONS; NONE; SPECIAL-PURPOSE MACHINES;

DISTRIBUTED PARAMETER NETWORKS; GENERAL PURPOSE COMPUTERS; HARDWARE; MOLECULAR DYNAMICS; SUPERCOMPUTERS;

DISTRIBUTED COMPUTER SYSTEMS;

EID: 84884855084     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/IPDPS.2013.93     Document Type: Conference Paper

References (53)

1. R. D. Fine, G. Dimmler, and C. Levinthal, "FASTRUN: A special purpose, hardwired computer for molecular simulation," Proteins, vol. 11, pp. 242-253, 1991.
2. M. Taiji, T. Narumi, Y. Ohno, N. Futatsugi, A. Suenaga, N. Takada, and A. Kanagaya, "Protein Explorer: a petaflops special purpose computer system for molecular dynamics simulations," Proc. ACM/IEEE Conf. on Supercomputing (SC03), New York, NY, 2003. ACM.
3. S. Toyoda, H. Miyagawa, K. Kitamura, T. Amisaki, E. Hashimoto, H. Ikeda, and N. Miyakawa, "Development of MD Engine: high-speed accelerator with parallel processor design for molecular dynamics simulations," J. Comput. Chem., vol. 20, pp. 185-199, 1999. (Pubitemid 129653027)
4. S. Habata, K. Umezawa, M. Yokokawa, and S. Kitawaki, "Hardware system of the Earth Simulator." Parallel. Comput., vol. 30, pp. 1287-1313, 2004.
5. J. Makino, E. Kokubo, and T. Fukushige, "Performance evaluation and tuning of GRAPE-6 - towards 40 'real' Tflops," Proc. ACM/IEEE Conf. on Supercomputing (SC03), New York, NY, 2003. ACM.
6. R. Perley, P. Napier, J. Jackson, B. Butler, B. Carlson, D. Fort, et al., "The expanded Very Large Array," Proc. IEEE, vol. 97, 1448-1462, 2009.
7. M. Awad, "FPGA supercomputing platforms: a survey," Proc. Intl. Conf. on Field Programmable Logic and Applications (FPL 2009), New York, NY, 2009. IEEE.
8. P. A. Boyle, D. Chen, N. H. Christ, M. A. Clark, S. D. Cohen, C. Cristian, et al., "Overview of the QCDSP and QCDOC computers," IBM J. Res. Dev., vol. 49, pp. 351-365, 2005.
9. J. D. Bakos, "High-performance heterogeneous computing with the Convey HC-1," Comput. Sci. Eng., vol. 12, pp. 80-87, 2010.
10. V. Heuveline and J.-P. Weiß, "Lattice Boltzmann methods on the ClearSpeed Advance™ accelerator board," Euro. Phys. J. Special Topics, vol. 171, pp. 31-36, 2009.
11. H. Baier, H. Boettiger, M. Drochner, N. Eicker, U. Fischer, Z. Fodor, et al., "QPACE: power-efficient parallel architecture based on IBM PowerXCell 8i," Comput. Sci. Res. Dev., vol. 25, pp. 149-154, 2010.
12. G. Goldrian, T. Huth, B. Krill, J. Lauritsen, H. Schick, I. Ouda, et al., "QPACE: quantum chromodynamics parallel computing on the Cell Broadband Engine," Comput. Sci. Eng. vol. 10, 46-54, 2008.
13. F. Belletti, M. Cotallo, A. Cruz, L. A. Fernández, A. Gordillo, M. Guidetti, et al., "JANUS: an FPGA-based system for high performance scientific computing," Comput. Sci. Eng. vol. 11, 48-58, 2009.
14. F. Belletti, M. Cotallo, A. Cruz, L. A. Fernández, A. Gordillo, A. Maiorano, et al., "IANUS: scientific computing on an FPGA-based architecture," in Parallel Computing: Architectures, Algorithms and Applications, vol. 38, C. Bischof, M. Bücker, P. Gibbon, G.R. Joubert, T. Lippert, B. Mohr, and F. Peters, Eds., Jülich: John von Neumann Institute for Computing, pp. 553-560, 2007.
15. F. Belletti, S. F. Schifano, R. Tripiccione, F. Bodin, P. Boucaud, J. Micheli, et al., "Computing for LQCD: apeNEXT," Comput. Sci. Eng. vol. 8, pp. 18-29, 2006.
16. P. Kogge, "The tops in flops," IEEE Spectrum, vol. 48, pp. 48-54, 2011.
17. D. E. Shaw, M. M. Deneroff, R. O. Dror, J. S. Kuskin, R. H. Larson, J. K. Salmon, et al., "Anton: a special-purpose machine for molecular dynamics simulation," Proc. 34th Annual Intl. Symp. on Computer Architecture (ISCA '07), New York, NY, 2007. ACM.
18. D. E. Shaw, R. O. Dror, J. K. Salmon, J.P. Grossman, K. M. Mackenzie, J. A. Bank, et al., "Millisecond-scale molecular dynamics simulations on Anton," Proc. Intl. Conf. for High Performance Computing, Networking, Storage and Analysis (SC09), New York, NY, 2009. ACM.
19. R. H. Larson, J. K. Salmon, R. O. Dror, M. M. Deneroff, C. Young, J.P. Grossman, et al., "High-throughput pairwise point interactions in Anton, a specialized machine for molecular dynamics simulation," Proc. 14th Annual Intl. Symp. on High-Performance Computer Architecture (HPCA '08), New York, NY, 2008. IEEE.
20. J. S. Kuskin, C. Young, J.P. Grossman, B. Batson, M. M. Deneroff, R. O. Dror, and D. E. Shaw, "Incorporating flexibility in Anton, a specialized machine for molecular dynamics simulation," Proc. 14th Annual Intl. Symp. on High-Performance Computer Architecture (HPCA '08), New York, NY, 2008. IEEE.
21. R. O. Dror, J.P. Grossman, K. M. Mackenzie, B. Towles, E. Chow, J. K. Salmon, et al., "Exploiting 162-nanosecond end-to-end communication latency on Anton," Proc. Intl. Conf. for High Performance Computing, Networking, Storage and Analysis (SC10), Washington, D.C., 2010. IEEE.
22. R. O. Dror, A. C. Pan, D. H. Arlow, D. W. Borhani, P. Maragakis, Y. Shan, et al., "Pathway and mechanism of drug binding to G-protein-coupled receptors," Proc. Natl. Acad. Sci. USA, vol. 108, pp. 13118-13123, 2011.
23. Y. Shan, E. T. Kim, M. P. Eastwood, R. O. Dror, M. A. Seeliger, and D. E. Shaw, "How does a drug molecule find its target binding site?" J. Am. Chem. Soc., vol. 133, pp. 9181-9183, 2011.
24. A. C. Kruse, J. Hu, A. C. Pan, D. H. Arlow, D. M. Rosenbaum, E. Rosemond, et al., "Structure and dynamics of the M3 muscarinic acetylcholine receptor," Nature, vol. 482, pp. 552-556, 2012.
25. D. E. Shaw, P. Maragakis, K. Lindorff-Larsen, S. Piana, R. O. Dror, M. P. Eastwood, et al., "Atomic-level characterization of the structural dynamics of proteins," Science, vol. 330, pp. 341-346, 2010.
26. K. Lindorff-Larsen, S. Piana, R. O. Dror, and D. E. Shaw, "How fast-folding proteins fold," Science, vol. 334, pp. 517-520, 2011.
27. M. Ø. Jensen, V. Jogini, D. W. Borhani, A. E. Leffler, R. O. Dror, and D. E. Shaw, "Mechanism of voltage gating in potassium channels," Science, vol. 336, pp. 229-233, 2012.
28. M. Ø. Jensen, V. Jogini, M. P. Eastwood, D. E. Shaw, "Atomic-level simulation of current-voltage relationships in single-file ion channels," J. Gen. Phys., in press.
29. Y. Shan, M. P. Eastwood, X. Zhang, E. T. Kim, A. Arkhipov, R. O. Dror, et al., "Oncogenic mutations counteract intrinsic disorder in the EGFR kinase and promote receptor dimerization," Cell, vol. 149, pp. 860-870, 2012.
30. 2-adrenergic receptor," Proc. Natl. Acad. Sci. USA, vol. 108, pp. 18684-18689, 2011.
31. D. M. Rosenbaum, C. Zhang, J. A. Lyons, R. Holl, D. Aragao, D. H. Arlow, et al., "Structure and function of an irreversible agonist-β2 adrenoceptor complex," Nature, vol. 469, pp. 236-240, 2011.
32. Y. Shan, J. L. Klepeis, M. P. Eastwood, R. O. Dror, and D. E. Shaw, "Gaussian split Ewald: a fast Ewald mesh method for molecular simulation," J. Chem. Phys., vol. 122, pp. 054101:1-13, 2005.
33. M. Wilkes, "The best way to design an automatic computing machine," Report of Manchester University Computer Inaugural Conference, pp. 182-184, 1951.
34. P. H. Hunenberger, "Thermostat algorithms for molecular dynamics simulations," Adv. Polym. Sci., vol. 173, pp. 105-149, 2005.
35. J. K. Salmon, M. A. Moraes, R. O. Dror, and D. E. Shaw, "Parallel random numbers: as easy as 1, 2, 3," Proc. Intl. Conf. for High Performance Computing, Networking, Storage and Analysis (SC11), New York, NY, 2011. ACM.
36. G. J. Martyna, M. L. Klein, and M. Tuckerman, "Nosé-Hoover chains: the canonical ensemble via continuous dynamics," J. Chem. Phys., vol. 97, pp. 2635-2643, 1992.
37. R. A. Lippert, C. Predescu, D. Ierardi, M. P. Eastwood, Ron O. Dror, and D. E. Shaw, "Multi-phased integrator for constant temperature and pressure molecular dynamics simulations," under review.
38. D. M. Zuckerman, "Equilibrium sampling in biomolecular simulations," Annu. Rev. Biophys., vol. 40, pp. 41-62, 2011.
39. G. M. Torrie and J. P. Valleau, "Nonphysical sampling distributions in Monte Carlo free energy estimation: umbrella sampling," J. Comput. Phys., vol. 23, pp. 187-199, 1977.
40. H. Grubmüller, B. Heymann, and P. Tavan, "Ligand binding: molecular mechanics calculation of the streptavidin-biotin rupture force," Science, vol. 271, pp. 997-999, 1996. (Pubitemid 26066398)
41. S. Izrailev, S. Stepaniants, M. Balsera, Y. Oono, and K. Schulten, "Molecular dynamics study of unbinding of the avidin-biotin complex," Biophys J., vol. 72, pp. 1568-1581, 1997. (Pubitemid 27133097)
42. L. Maragliano and E. Vanden-Eijnden, "A temperature accelerated method for sampling free energy and determining reaction pathways in rare events simulations," Chem. Phys. Lett., vol. 426, pp. 168-175, 2006.
43. W. Kabsch, "A solution of the best rotation to relate two sets of vectors," Acta Crystallogr., vol. A32, pp. 922-923, 1976.
44. W. Kabsch, "A discussion of the solution for the best rotation to relate two sets of vectors," Acta Crystallogr., vol. A34, pp. 827-828, 1978.
45. E. Marinari and G. Parisi, "Simulated tempering: a new Monte Carlo scheme," Europhys. Lett., vol. 19, pp. 451-458, 1992.
46. Y. Sugita and Y. Okamoto, "Replica-exchange molecular dynamics method for protein folding," Chem. Phys. Lett., vol. 314, 1-2, 1999.
47. P. Atkins and J. de Paula, Atkins' Physical Chemistry, 8th ed., Oxford: Oxford UP, pp. 637.
48. E. Chow, C. A. Rendleman, K. J. Bowers, R. O. Dror, D. H. Hughes, J. Gullingsrud, F. D. Sacerdoti, and D. E. Shaw, "Desmond performance on a cluster of multicore processors." D. E. Shaw Research Technical Report DESRES/TR-2008-01. http://deshawresearch.com. 2008.
49. B. Roux, The membrane potential and its representation by a constant electric field in computer simulations. Biophys. J. vol. 95, pp. 4205-4216, 2008.
50. A. D. MacKerell Jr., M. Feig, and C. L. Brooks III, "Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations," J. Comput. Chem., vol. 25, pp. 1400-1415, 2004.
51. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, "Comparison of simple potential functions for simulating liquid water," J. Chem. Phys., vol. 79, pp. 926-935, 1983.
52. K. J. Bowers, E. Chow, H. Xu, R. O. Dror, M. P. Eastwood, B. A. Gregersen, et al., "Scalable algorithms for molecular dynamics simulations on commodity clusters," Proc. of the ACM/IEEE Conf. on Supercomputing (SC06), New York, NY, 2006. IEEE.
53. + channel," Nature, vol. 414, pp. 73-77, 2001.