메뉴 건너뛰기




Volumn , Issue , 2008, Pages 331-342

High-throughput pairwise point interactions in anton, a specialized machine for molecular dynamics simulation

Author keywords

[No Author keywords available]

Indexed keywords

APPLICATION SPECIFIC INTEGRATED CIRCUITS; COMPUTERS; DYNAMICS; FLOW INTERACTIONS; GENERAL PURPOSE COMPUTERS; MOLECULAR DYNAMICS; PARALLEL ALGORITHMS; PIPELINES; QUANTUM CHEMISTRY; SUPERCOMPUTERS;

EID: 57749191489     PISSN: 15300897     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/HPCA.2008.4658650     Document Type: Conference Paper
Times cited : (26)

References (27)
  • 1
    • 33646943202 scopus 로고    scopus 로고
    • Molecular Dynamics: Survey of Methods for Simulating the Activity of Proteins
    • S. A. Adcock and J. A. McCammon, Molecular Dynamics: Survey of Methods for Simulating the Activity of Proteins, Chem. Rev., 106: 1589-1615 (2006).
    • (2006) Chem. Rev , vol.106 , pp. 1589-1615
    • Adcock, S.A.1    McCammon, J.A.2
  • 2
    • 24044541353 scopus 로고
    • Design and Implementation of the Delft Molecular-Dynamics Processor
    • Academic Press, San Diego
    • A. F. Bakker and C. Bruin, Design and Implementation of the Delft Molecular-Dynamics Processor, in Special Purpose Computers, pp. 183-232 (Academic Press, San Diego, 1988).
    • (1988) Special Purpose Computers , pp. 183-232
    • Bakker, A.F.1    Bruin, C.2
  • 4
    • 34547139405 scopus 로고    scopus 로고
    • The Midpoint Method for Parallelization of Particle Simulations
    • K. J. Bowers, R. O. Dror, and D. E. Shaw, The Midpoint Method for Parallelization of Particle Simulations, J. Chem. Phys, 124: 184109 (2006).
    • (2006) J. Chem. Phys , vol.124 , pp. 184109
    • Bowers, K.J.1    Dror, R.O.2    Shaw, D.E.3
  • 5
    • 33846148305 scopus 로고    scopus 로고
    • Zonal Methods for the Parallel Execution of Range-Limited N-body Simulations
    • K. J. Bowers, R. O. Dror, and D. E. Shaw, Zonal Methods for the Parallel Execution of Range-Limited N-body Simulations, J. Comput. Phys., 221(1): 303-329 (2007).
    • (2007) J. Comput. Phys , vol.221 , Issue.1 , pp. 303-329
    • Bowers, K.J.1    Dror, R.O.2    Shaw, D.E.3
  • 6
    • 0041140017 scopus 로고
    • Simulations of Peptide Conformational Dynamics and Thermodynamics
    • C. L. Brooks and D. A. Case, Simulations of Peptide Conformational Dynamics and Thermodynamics, Chem. Rev., 93: 2487-2502 (1993).
    • (1993) Chem. Rev , vol.93 , pp. 2487-2502
    • Brooks, C.L.1    Case, D.A.2
  • 8
    • 0032561237 scopus 로고    scopus 로고
    • Pathways to a Protein Folding Intermediate Observed in a 1-Microsecond Simulation in Aqueous Solution
    • Y. Duan and P. A. Kollman, Pathways to a Protein Folding Intermediate Observed in a 1-Microsecond Simulation in Aqueous Solution, Science, 282(5389): 740-744 (1998).
    • (1998) Science , vol.282 , Issue.5389 , pp. 740-744
    • Duan, Y.1    Kollman, P.A.2
  • 9
    • 0026342528 scopus 로고    scopus 로고
    • R. D. Fine, G. Dimmler, and C. Levinthal, FASTRUN: A Special Purpose, Hardwired Computer for Molecular Simulation, Proteins: Struct. Funct. Genet., 11(4): 242-253, 1991 (erratum: 14(3): 421-422, 1992).
    • R. D. Fine, G. Dimmler, and C. Levinthal, FASTRUN: A Special Purpose, Hardwired Computer for Molecular Simulation, Proteins: Struct. Funct. Genet., 11(4): 242-253, 1991 (erratum: 14(3): 421-422, 1992).
  • 11
    • 33746603053 scopus 로고    scopus 로고
    • B. G. Fitch, A. Rayshubskiy, M. Eleftheriou, T.J. Christopher Ward, M. Giampapa, Y. Zhestkov, M. C. Pitman, F. Suits, A. Grossfield, J. Pitera, W. Swope, R. Zhou, S. Feller, and R. S. Germain, Blue Matter: Strong Scaling of Molecular Dynamics on Blue Gene/L, in Proceedings of the International Conference on Computational Science (ICCS 2006), V. Alexandrov, D. van Albada, P. Sloot, and J. Dongarra, Eds., Springer-Verlag, LNCS, 3992:846-854 (2006).
    • B. G. Fitch, A. Rayshubskiy, M. Eleftheriou, T.J. Christopher Ward, M. Giampapa, Y. Zhestkov, M. C. Pitman, F. Suits, A. Grossfield, J. Pitera, W. Swope, R. Zhou, S. Feller, and R. S. Germain, Blue Matter: Strong Scaling of Molecular Dynamics on Blue Gene/L, in Proceedings of the International Conference on Computational Science (ICCS 2006), V. Alexandrov, D. van Albada, P. Sloot, and J. Dongarra, Eds., Springer-Verlag, LNCS, 3992:846-854 (2006).
  • 13
    • 0036725277 scopus 로고    scopus 로고
    • Molecular Dynamics Simulations of Biomolecules
    • M. Karplus and J. A. McCammon, Molecular Dynamics Simulations of Biomolecules, Nat. Struct. Bio., 9(9):646-652 (2002).
    • (2002) Nat. Struct. Bio , vol.9 , Issue.9 , pp. 646-652
    • Karplus, M.1    McCammon, J.A.2
  • 15
    • 57749176501 scopus 로고    scopus 로고
    • MD Benchmarks for Amber, CHARMM and NAMD, See
    • MD Benchmarks for Amber, CHARMM and NAMD, See http://amber.scripps.edu/ amber8.bench2.html.
  • 18
    • 0002467378 scopus 로고
    • Fast Parallel Algorithms for Short-Range Molecular-Dynamics
    • S. Plimpton, Fast Parallel Algorithms for Short-Range Molecular-Dynamics, J. Comput. Phys., 117(1): 1-19 (1995).
    • (1995) J. Comput. Phys , vol.117 , Issue.1 , pp. 1-19
    • Plimpton, S.1
  • 19
    • 85190300254 scopus 로고    scopus 로고
    • T. Schlick, R. D. Skeel, A. T. Brunger, L. V. Kalé, J. A. Board, J. Hermans, and K. Schulten, Algorithmic Challenges in Computational Molecular Biophysics, J. Comput. Phys., 151(1): 9-48 (1999).
    • T. Schlick, R. D. Skeel, A. T. Brunger, L. V. Kalé, J. A. Board, J. Hermans, and K. Schulten, Algorithmic Challenges in Computational Molecular Biophysics, J. Comput. Phys., 151(1): 9-48 (1999).
  • 20
    • 27344455346 scopus 로고    scopus 로고
    • Reproducible Polypeptide Folding and Structure Prediction Using Molecular Dynamics Simulations
    • M. M. Seibert, A. Patriksson, B. Hess, and D. van der Spoel, Reproducible Polypeptide Folding and Structure Prediction Using Molecular Dynamics Simulations, J. Mol. Biol., 354(1): 173-183 (2005).
    • (2005) J. Mol. Biol , vol.354 , Issue.1 , pp. 173-183
    • Seibert, M.M.1    Patriksson, A.2    Hess, B.3    van der Spoel, D.4
  • 21
    • 22944460220 scopus 로고    scopus 로고
    • Gaussian Split Ewald: A Fast Ewald Mesh Method for Molecular Simulation
    • 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., 122:054101 (2005).
    • (2005) J. Chem. Phys , vol.122 , pp. 054101
    • Shan, Y.1    Klepeis, J.L.2    Eastwood, M.P.3    Dror, R.O.4    Shaw, D.E.5
  • 22
    • 24144495573 scopus 로고    scopus 로고
    • Scalable Method for the Parallel Evaluation of Distance-Limited Pairwise Particle Interactions
    • D. E. Shaw. A Fast, Scalable Method for the Parallel Evaluation of Distance-Limited Pairwise Particle Interactions, J. Comput. Chem., 26:1318-1328 (2005).
    • (2005) J. Comput. Chem , vol.26 , pp. 1318-1328
    • Shaw, D.E.1    Fast, A.2
  • 23
    • 35348886062 scopus 로고    scopus 로고
    • D. E. Shaw, M. M. Deneroff, R. O. Dror, J. S. Kuskin, R. H. Larson, J. K. Salmon, C. Young, B. Batson, K. J. Bowers, J. C. Chao, M. P. Eastwood, J. Gagliardo, J.P. Grossman, C. R. Ho, D. J. Ierardi, I. Kolossváry, J. L. Klepeis, T. Layman, C. McLeavey, M. A. Moraes, R. Mueller, E. C. Priest, Y. Shan, J. Spengler, M. Theobald, B. Towles, S. C. Wang, Anton: A Special-Purpose Machine for Molecular Dynamics Simulation, in Proc. 34th International Symposium on Computer Architecture (ISCA'07), 1-12, San Diego, CA, 2007.
    • D. E. Shaw, M. M. Deneroff, R. O. Dror, J. S. Kuskin, R. H. Larson, J. K. Salmon, C. Young, B. Batson, K. J. Bowers, J. C. Chao, M. P. Eastwood, J. Gagliardo, J.P. Grossman, C. R. Ho, D. J. Ierardi, I. Kolossváry, J. L. Klepeis, T. Layman, C. McLeavey, M. A. Moraes, R. Mueller, E. C. Priest, Y. Shan, J. Spengler, M. Theobald, B. Towles, S. C. Wang, Anton: A Special-Purpose Machine for Molecular Dynamics Simulation, in Proc. 34th International Symposium on Computer Architecture (ISCA'07), 1-12, San Diego, CA, 2007.
  • 24
    • 1642632943 scopus 로고    scopus 로고
    • N-Body Computations with Cutoffs
    • M. Snir, A Note on N-Body Computations with Cutoffs, Theor. Comput. Syst., 37: 295-318 (2004).
    • (2004) Theor. Comput. Syst , vol.37 , pp. 295-318
    • Snir, M.1    Note on, A.2
  • 26
    • 0001700958 scopus 로고    scopus 로고
    • High-Speed Accelerator with Parallel Processor Design for Molecular Dynamics Simulations
    • Development of MD Engine
    • S. Toyoda, H. Miyagawa, K. Kitamura, T. Amisaki, E. Hashimoto, H. Ikeda, A. Kusumi, and N. Miyakawa, Development of MD Engine: High-Speed Accelerator with Parallel Processor Design for Molecular Dynamics Simulations, J. Comput. Chem., 20(2): 185-199 (1999)
    • (1999) J. Comput. Chem , vol.20 , Issue.2 , pp. 185-199
    • Toyoda, S.1    Miyagawa, H.2    Kitamura, K.3    Amisaki, T.4    Hashimoto, E.5    Ikeda, H.6    Kusumi, A.7    Miyakawa, N.8


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.