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Volumn 63, Issue 7-8, 2003, Pages 759-773

Blue Matter, an application framework for molecular simulation on Blue Gene

Author keywords

Biomolecular simulation; Molecular dynamics; N body problem; Parallel computing

Indexed keywords


EID: 0142010565     PISSN: 07437315     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0743-7315(03)00084-4     Document Type: Article
Times cited : (57)

References (30)
  • 1
    • 0034958341 scopus 로고    scopus 로고
    • Blue Gene: A vision for protein science using a petaflop supercomputer
    • F. Allen, et al., Blue Gene: a vision for protein science using a petaflop supercomputer, IBM Systems J. 40 (2) (2001) 310-327.
    • (2001) IBM Systems J. , vol.40 , Issue.2 , pp. 310-327
    • Allen, F.1
  • 2
    • 12444309581 scopus 로고    scopus 로고
    • An overview of the Blue Gene/L supercomputer
    • Supercomputing 2002 Proceedings
    • N. Adiga, et al., An overview of the Blue Gene/L supercomputer, in: Supercomputing 2002 Proceedings, 2002, http://www.sc2002.org/paperpdfs/pap.pap207.pdf.
    • (2002)
    • Adiga, N.1
  • 3
    • 0003438164 scopus 로고    scopus 로고
    • Generic Programming and the STL: Using and Extending the C++ Standard Template Library
    • Addison-Wesley, Reading, MA
    • M. Austern, Generic Programming and the STL: Using and Extending the C++ Standard Template Library, Addison-Wesley, Reading, MA, 1999.
    • (1999)
    • Austern, M.1
  • 4
    • 0000476256 scopus 로고
    • Computer simulation study of the mean forces between ferrous and ferric ions in water
    • J. Bader, D. Chandler, Computer simulation study of the mean forces between ferrous and ferric ions in water, J. Phys. Chem. 96 (1992) 6423-6427.
    • (1992) J. Phys. Chem. , vol.96 , pp. 6423-6427
    • Bader, J.1    Chandler, D.2
  • 7
    • 0001786236 scopus 로고
    • Simulation of electrostatic systems in periodic boundary conditions I. lattice sums and dielectric constants
    • and references therein
    • S. De Leeuw, J. Perram, E. Smith, Simulation of electrostatic systems in periodic boundary conditions I. lattice sums and dielectric constants, Proc. Roy. Soc. Lond. A 373 (1980) 27-56 and references therein.
    • (1980) Proc. Roy. Soc. Lond. A , vol.373 , pp. 27-56
    • De Leeuw, S.1    Perram, J.2    Smith, E.3
  • 8
    • 0032561237 scopus 로고    scopus 로고
    • Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
    • Y. Duan, P. Kollman, Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution, Science 282 (1998) 740.
    • (1998) Science , vol.282 , pp. 740
    • Duan, Y.1    Kollman, P.2
  • 9
    • 0004722604 scopus 로고
    • The vulcan operating environment: A brief overview and status report
    • G.-R. Hoffman, T. Kauranne (Eds.), World Scientific, Singapore
    • B. Fitch, M. Giampapa, The vulcan operating environment: a brief overview and status report, in: G.-R. Hoffman, T. Kauranne (Eds.), Parallel Supercomputing in Atmospheric Science, World Scientific, Singapore, 1993, p. 130.
    • (1993) Parallel Supercomputing in Atmospheric Science , pp. 130
    • Fitch, B.1    Giampapa, M.2
  • 11
    • 0000396658 scopus 로고
    • A fast algorithm for particle simulations
    • L. Greengard, V. Rokhlin, A fast algorithm for particle simulations, J. Comput. Phys. 73 (1987) 325-348.
    • (1987) J. Comput. Phys. , vol.73 , pp. 325-348
    • Greengard, L.1    Rokhlin, V.2
  • 12
    • 0003569545 scopus 로고
    • Computer Simulation Using Particles
    • Institute of Physics Publishing, UK
    • R. Hockney, J. Eastwood, Computer Simulation Using Particles, Institute of Physics Publishing, UK, 1988.
    • (1988)
    • Hockney, R.1    Eastwood, J.2
  • 13
    • 85030955609 scopus 로고    scopus 로고
    • Impact
    • Impact, http://www.schrodinger.com.
  • 14
    • 0036725277 scopus 로고    scopus 로고
    • Molecular dynamics simulations of biomolecules
    • M. Karplus, J. McCammon, Molecular dynamics simulations of biomolecules, Nat. Struct. Biol. 9 (9) (2002) 646-652.
    • (2002) Nat. Struct. Biol. , vol.9 , Issue.9 , pp. 646-652
    • Karplus, M.1    McCammon, J.2
  • 15
    • 34547887373 scopus 로고
    • Summation of Coulomb fields in computer-simulated disordered systems
    • J. Lekner, Summation of Coulomb fields in computer-simulated disordered systems, Physics A 176 (1991) 485-498.
    • (1991) Physics A , vol.176 , pp. 485-498
    • Lekner, J.1
  • 18
    • 34447324237 scopus 로고    scopus 로고
    • NAMD: Biomolecular simulation on thousands of processors
    • Supercomputing 2002 Proceedings
    • J. Phillips, G. Zheng, S. Kumar, L. Kale, NAMD: biomolecular simulation on thousands of processors, in: Supercomputing 2002 Proceedings, 2002, http://www.sc2002.org/paperpdfs/pap.pap277.pdf.
    • (2002)
    • Phillips, J.1    Zheng, G.2    Kumar, S.3    Kale, L.4
  • 19
    • 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 (1995) 1-19.
    • (1995) J. Comput. Phys. , vol.117 , pp. 1-19
    • Plimpton, S.1
  • 20
    • 23544482118 scopus 로고    scopus 로고
    • Tiling optimizations for 3d scientific computations
    • Supercomputing, 2000 Proceedings
    • G. Rivera, C.-W. Tseng, Tiling optimizations for 3d scientific computations, Supercomputing, 2000 Proceedings, 2000, http://www.cs.umd.edu/projects/cosmic/papers/sc00.ps.
    • (2000)
    • Rivera, G.1    Tseng, C.-W.2
  • 21
    • 0032080053 scopus 로고    scopus 로고
    • Calculations on folding of segment b1 of streptococcal protein g
    • F. Sheinerman, C. Brooks III, Calculations on folding of segment b1 of streptococcal protein g, J. Mol. Biol. 278 (1998) 439-456.
    • (1998) J. Mol. Biol. , vol.278 , pp. 439-456
    • Sheinerman, F.1    Brooks III, C.2
  • 22
    • 0037038372 scopus 로고    scopus 로고
    • Absolute comparison of simulated and experimental protein-folding dynamics
    • (6911)
    • C. Snow, H. Nguyen, V. Pande, M. Gruebele, Absolute comparison of simulated and experimental protein-folding dynamics, Nature 420 (6911) (2002) 102-106.
    • (2002) Nature , vol.420 , pp. 102-106
    • Snow, C.1    Nguyen, H.2    Pande, V.3    Gruebele, M.4
  • 23
    • 0142045520 scopus 로고    scopus 로고
    • An alternative to Ewald sums, Part 2: The Coulomb potential in a periodic system
    • R. Sperb, An alternative to Ewald sums, Part 2: the Coulomb potential in a periodic system, Mol. Simul. 23 (1999) 199-212.
    • (1999) Mol. Simul. , vol.23 , pp. 199-212
    • Sperb, R.1
  • 24
    • 0002504626 scopus 로고    scopus 로고
    • An alternative to Ewald sums part 3: Implementation and results
    • R. Strebel, R. Sperb, An alternative to Ewald sums part 3: implementation and results, Mol. Simul. 27 (2001) 61-74.
    • (2001) Mol. Simul. , vol.27 , pp. 61-74
    • Strebel, R.1    Sperb, R.2
  • 25
    • 0000522680 scopus 로고    scopus 로고
    • Parallel molecular dynamics: Implications for massively parallel machines
    • V. Taylor, R. Stevens, K. Arnold, Parallel molecular dynamics: implications for massively parallel machines, J. Parallel and Distrib. Comput. 45 (2) (1997) 166-175.
    • (1997) J. Parallel and Distrib. Comput. , vol.45 , Issue.2 , pp. 166-175
    • Taylor, V.1    Stevens, R.2    Arnold, K.3
  • 26
    • 33646650705 scopus 로고
    • Reversible multiple time scale molecular dynamics
    • M. Tuckerman, B. Berne, G. Martyna, Reversible multiple time scale molecular dynamics, J. Chem. Phys. 97 (3) (1992) 1990-2001.
    • (1992) J. Chem. Phys. , vol.97 , Issue.3 , pp. 1990-2001
    • Tuckerman, M.1    Berne, B.2    Martyna, G.3
  • 28
    • 0001349174 scopus 로고    scopus 로고
    • Validation of molecular dynamics simulation
    • W. van Gunsteren, A. Mark, Validation of molecular dynamics simulation, J. Chem. Phys. 108 (15) (1998) 6109-6116.
    • (1998) J. Chem. Phys. , vol.108 , Issue.15 , pp. 6109-6116
    • van Gunsteren, W.1    Mark, A.2
  • 29
    • 0036789950 scopus 로고    scopus 로고
    • Can a continuum solvent model reproduce the free energy landscape of a beta-hairpin folding in water?
    • R. Zhou, B. Berne, Can a continuum solvent model reproduce the free energy landscape of a beta-hairpin folding in water?, Proc. Natl. Acad. Sci. USA 99 (20) (2002) 12777-12782.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , Issue.20 , pp. 12777-12782
    • Zhou, R.1    Berne, B.2
  • 30
    • 0035424713 scopus 로고    scopus 로고
    • Efficient multiple time step method for use with Ewald and particle mesh Ewald for large biomolecular systems
    • R. Zhou, E. Harder, H. Xu, B. Berne, Efficient multiple time step method for use with Ewald and particle mesh Ewald for large biomolecular systems, J. Chem. Phys. 115 (5) (2001) 2348-2358.
    • (2001) J. Chem. Phys. , vol.115 , Issue.5 , pp. 2348-2358
    • Zhou, R.1    Harder, E.2    Xu, H.3    Berne, B.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.