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Volumn 45, Issue 6, 2005, Pages 1600-1604

Symplectic molecular dynamics simulations on specially designed parallel computers

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; INTEGRATION; MOLECULAR VIBRATIONS; NATURAL FREQUENCIES; PARALLEL PROCESSING SYSTEMS; PROGRAM PROCESSORS;

EID: 29044447721     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci050216q     Document Type: Conference Paper
Times cited : (25)

References (31)
  • 3
    • 1642357706 scopus 로고    scopus 로고
    • The many roles of computation in drug discovery
    • Jorgensen, W. L. The many roles of computation in drug discovery. Science 2004, 303, 1812-1818.
    • (2004) Science , vol.303 , pp. 1812-1818
    • Jorgensen, W.L.1
  • 5
    • 2142813682 scopus 로고
    • Computer simulation of molecular dynamics" Methodology, applications, and perspectives in chemistry
    • van Gunsteren, W. F.; Berendsen, H. J. C. Computer simulation of molecular dynamics" Methodology, applications, and perspectives in chemistry. Angew. Chem., Int. Ed. 1990, 29, 992-1023.
    • (1990) Angew. Chem., Int. Ed. , vol.29 , pp. 992-1023
    • Van Gunsteren, W.F.1    Berendsen, H.J.C.2
  • 6
    • 0030918284 scopus 로고    scopus 로고
    • Biomolecular dynamics at long timesteps" Bridging the timescale gap between simulation and experimentation
    • Schlick, T.; Earth, E.; Mandziuk, M. Biomolecular dynamics at long timesteps" Bridging the timescale gap between simulation and experimentation. Annu. Rev. Biophys. Biomol. Struct. 1997, 26, 181-222.
    • (1997) Annu. Rev. Biophys. Biomol. Struct. , vol.26 , pp. 181-222
    • Schlick, T.1    Earth, E.2    Mandziuk, M.3
  • 7
    • 18744367282 scopus 로고    scopus 로고
    • Molecular dynamics integration and molecular vibrational theory. I. New symplectic integrators
    • Janežič, D.; Praprotnik, M.; Merzel, F. Molecular dynamics integration and molecular vibrational theory. I. New symplectic integrators. J. Chem. Phys. 2005, 122, 174101.
    • (2005) J. Chem. Phys. , vol.122 , pp. 174101
    • Janežič, D.1    Praprotnik, M.2    Merzel, F.3
  • 8
    • 18744417282 scopus 로고    scopus 로고
    • Molecular dynamics integration and molecular vibrational theory. II. Simulation of non-linear molecules
    • Praprotnik, M.; Janežič, D. Molecular dynamics integration and molecular vibrational theory. II. Simulation of non-linear molecules. J. Chem. Phys. 2005, 122, 174102.
    • (2005) J. Chem. Phys. , vol.122 , pp. 174102
    • Praprotnik, M.1    Janežič, D.2
  • 9
    • 18744373063 scopus 로고    scopus 로고
    • Molecular dynamics integration and molecular vibrational theory. III. The IR spectrum of water
    • Praprotnik, M.; Janežič, D. Molecular dynamics integration and molecular vibrational theory. III. The IR spectrum of water. J. Chem. Phys. 2005, 122, 174103.
    • (2005) J. Chem. Phys. , vol.122 , pp. 174103
    • Praprotnik, M.1    Janežič, D.2
  • 10
    • 29044451097 scopus 로고
    • Parallel molecular dynamics algorithms for simulation of molecular systems
    • Mattson, T. G., Ed.; Symposium Series 592 American Chemical Society
    • Plimpton, S.; Hendrickson, B. Parallel Molecular Dynamics Algorithms for Simulation of Molecular Systems. In Parallel Computing in Computational Chemistry-, Mattson, T. G., Ed.; Symposium Series 592 American Chemical Society" 1995.
    • (1995) Parallel Computing in Computational Chemistry
    • Plimpton, S.1    Hendrickson, B.2
  • 12
  • 15
    • 0030216330 scopus 로고    scopus 로고
    • Improved schemes for mapping arbitrary algorithms onto processor meshes
    • Robič, B.; Vilfan, B. Improved schemes for mapping arbitrary algorithms onto processor meshes. Parallel Computing 1996, 22, 701-724.
    • (1996) Parallel Computing , vol.22 , pp. 701-724
    • Robič, B.1    Vilfan, B.2
  • 16
    • 34548268724 scopus 로고    scopus 로고
    • An 8.61 Tflop/s molecular dynamics simulation for NaCl with a special-purpose computer" MDM
    • Denver
    • Narumi, T.; Kawai, A.; Koishi, T. An 8.61 Tflop/s Molecular Dynamics Simulation for NaCl with a Special-Purpose Computer" MDM. In Proceedings of SuperComputing 2001; Denver, 2001.
    • (2001) Proceedings of SuperComputing 2001
    • Narumi, T.1    Kawai, A.2    Koishi, T.3
  • 18
    • 0001099087 scopus 로고    scopus 로고
    • Molecular dynamics machine" Special-purpose computer for molecular dynamics simulations
    • Narumi, T.; Susukita, R.; Ebisuzaki, T.; McNiven, G.; Elmegreen, B. Molecular dynamics machine" Special-purpose computer for molecular dynamics simulations. Mol. Simul. 1999, 21, 401-415.
    • (1999) Mol. Simul. , vol.21 , pp. 401-415
    • Narumi, T.1    Susukita, R.2    Ebisuzaki, T.3    McNiven, G.4    Elmegreen, B.5
  • 21
    • 0029276252 scopus 로고
    • An efficient symplectic integration algorithm for molecular dynamics simulations
    • Janežič, D.; Merzel, F. An efficient symplectic integration algorithm for molecular dynamics simulations. J. Chem. Inf. Comput. Sci. 1995, 35, 321-326.
    • (1995) J. Chem. Inf. Comput. Sci. , vol.35 , pp. 321-326
    • Janežič, D.1    Merzel, F.2
  • 22
    • 0032737545 scopus 로고    scopus 로고
    • Symplectic variable step size integration for N-body problems
    • Hardy, D. J.; Okunbor, D. I.; Skeel, R. D. Symplectic variable step size integration for N-body problems. Appl. Numer. Math. 1999, 29, 19-30.
    • (1999) Appl. Numer. Math. , vol.29 , pp. 19-30
    • Hardy, D.J.1    Okunbor, D.I.2    Skeel, R.D.3
  • 23
    • 0000885331 scopus 로고
    • Harmonic analysis of large systems. I. Methodology
    • Brooks, B. R.; Janežič, D.; Karplus, M. Harmonic analysis of large systems. I. Methodology. J. Comput. Chem. 1995, 16, 1522-1542.
    • (1995) J. Comput. Chem. , vol.16 , pp. 1522-1542
    • Brooks, B.R.1    Janežič, D.2    Karplus, M.3
  • 24
    • 84986469420 scopus 로고
    • Harmonic analysis of large systems. II. Comparison of different protein models
    • Janežič, D.; Brooks, B. R. Harmonic analysis of large systems. II. Comparison of different protein models. J. Comput. Chem. 1995, 16, 1543-1553.
    • (1995) J. Comput. Chem. , vol.16 , pp. 1543-1553
    • Janežič, D.1    Brooks, B.R.2
  • 25
    • 84986473952 scopus 로고
    • Harmonic analysis of large systems. III. Comparison with molecular dynamics
    • Janežič, D.; Venable, R. M.; Brooks, B. R. Harmonic analysis of large systems. III. Comparison with molecular dynamics. J. Comput. Chem. 1995, 16, 1554-1566.
    • (1995) J. Comput. Chem. , vol.16 , pp. 1554-1566
    • Janežič, D.1    Venable, R.M.2    Brooks, B.R.3
  • 26
    • 0001030772 scopus 로고    scopus 로고
    • Split integration symplectic method for molecular dynamics integration
    • Janežič, D.; Merzel, F. Split integration symplectic method for molecular dynamics integration. J. Chem. Inf. Comput. Sci. 1997, 37, 1048-1054.
    • (1997) J. Chem. Inf. Comput. Sci. , vol.37 , pp. 1048-1054
    • Janežič, D.1    Merzel, F.2
  • 27
    • 22944467757 scopus 로고
    • Computer "experiments" on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules
    • Verlet, L. Computer "experiments" on classical fluids. I. thermodynamical properties of Lennard-Jones molecules. Phys. Rev. 1967, 159, 98-103.
    • (1967) Phys. Rev. , vol.159 , pp. 98-103
    • Verlet, L.1
  • 28
    • 0000042162 scopus 로고    scopus 로고
    • A new parallel method for molecular dynamics simulation of macromolecular systems
    • Plimpton, S.; Hendrickson, B. A new parallel method for molecular dynamics simulation of macromolecular systems. J. Comput. Chem. 1998, 17, 326-337.
    • (1998) J. Comput. Chem. , vol.17 , pp. 326-337
    • Plimpton, S.1    Hendrickson, B.2
  • 29
    • 1842690027 scopus 로고    scopus 로고
    • Improving the performance of molecular dynamics simulations on parallel clusters
    • Borštnik, U.; Hodošček, M.; Janežič, D. Improving the performance of molecular dynamics simulations on parallel clusters. J. Chem. Inf. Comput. Sci. 2004, 44, 359-364.
    • (2004) J. Chem. Inf. Comput. Sci. , vol.44 , pp. 359-364
    • Borštnik, U.1    Hodošček, M.2    Janežič, D.3
  • 30
    • 0033100655 scopus 로고    scopus 로고
    • Efficient parallel algorithms for molecular dynamics simulations
    • Murty, R.; Okunbor, D. Efficient parallel algorithms for molecular dynamics simulations. Parallel Computing 1999, 25, 217-230.
    • (1999) Parallel Computing , vol.25 , pp. 217-230
    • Murty, R.1    Okunbor, D.2
  • 31
    • 1642632943 scopus 로고    scopus 로고
    • A note on n-body computations with cutoffs
    • Snir, M. A note on n-body computations with cutoffs. Theory Comput. Systems 2004, 37, 295-318.
    • (2004) Theory Comput. Systems , vol.37 , pp. 295-318
    • Snir, M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.