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Volumn 37, Issue 6, 1997, Pages 1055-1062

The complexity of parallel symplectic molecular dynamics algorithms

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EID: 0001363956     PISSN: 00952338     EISSN: None     Source Type: Journal    
DOI: 10.1021/ci970226u     Document Type: Article
Times cited : (10)

References (35)
  • 4
    • 0030918284 scopus 로고    scopus 로고
    • Biomolecular Dynamics at Long Timesteps: Bridging the Timescale Gap between Simulation and Experimentation
    • Stroud, R. M., Ed. and references cited therein
    • Schlick, T.; Barth, E.; Mandziuk, M. Biomolecular Dynamics at Long Timesteps: Bridging the Timescale Gap Between Simulation and Experimentation; Stroud, R. M., Ed. Annu. Rev. Biophys. Biomol. Struct. 1997, 26, and references cited therein.
    • (1997) Annu. Rev. Biophys. Biomol. Struct. , vol.26
    • Schlick, T.1    Barth, E.2    Mandziuk, M.3
  • 5
    • 0343087410 scopus 로고
    • Integration Methods for Molecular Dynamics
    • Mesirov, J., Schulten, K., Eds,; Springer-Verlag: Berlin
    • Leimkuhler, B. J.; Reich, S.; Skeel, R. D. Integration Methods for Molecular Dynamics. In IMA Volumes in Mathematics and its Applications; Mesirov, J., Schulten, K., Eds,; Springer-Verlag: Berlin, 1995; Vol. 82.
    • (1995) IMA Volumes in Mathematics and Its Applications , vol.82
    • Leimkuhler, B.J.1    Reich, S.2    Skeel, R.D.3
  • 6
    • 22944467757 scopus 로고
    • Computer "Experiments" on Classical Fluids. I. Thermo-dynamical Properties of Lennard-Jones Molecules
    • Verlet, L. Computer "Experiments" on Classical Fluids. I. Thermo-dynamical Properties of Lennard-Jones Molecules. Phys. Rev. 1967, 159, 98-103.
    • (1967) Phys. Rev. , vol.159 , pp. 98-103
    • Verlet, L.1
  • 7
    • 84952104504 scopus 로고
    • An Analysis of the Accuracy of Langevin and Molecular Dynamics Algorithms
    • Pastor, R. W.; Brooks, B. R.; Szabo, A. An Analysis of the Accuracy of Langevin and Molecular Dynamics Algorithms. Mol. Phys. 1988, 65, 1409-1419.
    • (1988) Mol. Phys. , vol.65 , pp. 1409-1419
    • Pastor, R.W.1    Brooks, B.R.2    Szabo, A.3
  • 8
    • 0000240098 scopus 로고
    • Dynamics of Molecules with Internal Degrees of Freedom by Multiple Time-Step Methods
    • Watanabe, M.; Karplus, M. Dynamics of Molecules with Internal Degrees of Freedom by Multiple Time-Step Methods. J. Chem. Phys. 1993, 99, 8063-8074.
    • (1993) J. Chem. Phys. , vol.99 , pp. 8063-8074
    • Watanabe, M.1    Karplus, M.2
  • 9
    • 0027658461 scopus 로고
    • Parallel Algorithm for Molecular Dynamics Integration
    • Trobec, R.; Jerebic, I.; D. Janežič, D. Parallel Algorithm for Molecular Dynamics Integration. Parallel Comput. 1993, 19, 1029-1039.
    • (1993) Parallel Comput. , vol.19 , pp. 1029-1039
    • Trobec, R.1    Jerebic, I.2    D. Janežič, D.3
  • 10
    • 84990557178 scopus 로고
    • Molecular Dynamics by the Backward Euler Method
    • Peskin, C. S.; Schlick, T. Molecular Dynamics by the Backward Euler Method. Comm. Pure. Appl. Math. 1989, 42, 1001-1031.
    • (1989) Comm. Pure. Appl. Math. , vol.42 , pp. 1001-1031
    • Peskin, C.S.1    Schlick, T.2
  • 11
    • 0142080331 scopus 로고
    • On Increasing the Time Step in Molecular Dynamics
    • Nyberg, A. M.; Schlick, T. On Increasing the Time Step in Molecular Dynamics. Chem. Phys. Lett. 1992, 98, 538.
    • (1992) Chem. Phys. Lett. , vol.98 , pp. 538
    • Nyberg, A.M.1    Schlick, T.2
  • 12
    • 84986483801 scopus 로고
    • A Truncated Newton Minimizer Adapted for CHARMM and Biomolecular Applications
    • Derreumaux, P.; Zhang, G.; Schlick, T.; Brooks, B. R. A Truncated Newton Minimizer Adapted for CHARMM and Biomolecular Applications. J. Comput. Chem. 1994, 15, 532-555.
    • (1994) J. Comput. Chem. , vol.15 , pp. 532-555
    • Derreumaux, P.1    Zhang, G.2    Schlick, T.3    Brooks, B.R.4
  • 13
    • 0038976122 scopus 로고
    • Runge-Kutta Schemes for Hamiltonian Systems
    • Sanz-Serna, J. M. Runge-Kutta Schemes for Hamiltonian Systems. BIT 1988, 28, 877-883.
    • (1988) BIT , vol.28 , pp. 877-883
    • Sanz-Serna, J.M.1
  • 15
    • 0010353041 scopus 로고
    • Implicit Runge-Kutta Method for Molecular Dynamics Integration
    • Janežič, D.; Orel, B. Implicit Runge-Kutta Method for Molecular Dynamics Integration. J. Chem. Inf. Comput. Sci. 1993, 33, 252-257.
    • (1993) J. Chem. Inf. Comput. Sci. , vol.33 , pp. 252-257
    • Janežič, D.1    Orel, B.2
  • 16
    • 84987093709 scopus 로고
    • Improvement of Methods for Molecular Dynamics Integration
    • Janežič, D.; Orel, B. Improvement of Methods for Molecular Dynamics Integration. Int. J. Quantum. Chem. 1994, 51, 407-415.
    • (1994) Int. J. Quantum. Chem. , vol.51 , pp. 407-415
    • Janežič, D.1    Orel, B.2
  • 17
    • 0028426291 scopus 로고
    • Parallelization of an Implicit Runge-Kutta Method for Molecular Dynamics Integration
    • Janežič, D.; Trobec, R. Parallelization of an Implicit Runge-Kutta Method for Molecular Dynamics Integration. J. Chem. Inf. Comput. Sci. 1994, 34, 641-646.
    • (1994) J. Chem. Inf. Comput. Sci. , vol.34 , pp. 641-646
    • Janežič, D.1    Trobec, R.2
  • 18
    • 0029208421 scopus 로고
    • Comparison of Parallel Verlet and Implicit Runge-Kutta Methods for Molecular Dynamics Integration
    • Trobec, R.; Janežič, D. Comparison of Parallel Verlet and Implicit Runge-Kutta Methods for Molecular Dynamics Integration. J. Chem. Inf. Comput. Sci. 1995, 35, 100-105.
    • (1995) J. Chem. Inf. Comput. Sci. , vol.35 , pp. 100-105
    • Trobec, R.1    Janežič, D.2
  • 19
    • 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
  • 20
    • 85033173342 scopus 로고    scopus 로고
    • Molecular Dynamics Simulations of Macromolecules: Improvements on Computational Efficiency
    • Trobec, R., Vajteršič, M., Zinterhof, P., Šilc, J., Robič, B., Eds.; Institute Jožef Stefan: Ljubljana, Slovenia, (ISBN 86-80023-25-6)
    • Janežič, D.; Merzel, F. Molecular Dynamics Simulations of Macromolecules: Improvements on Computational Efficiency. In Proceedings of the International Workshop PARALLEL NUMERICS '96; Trobec, R., Vajteršič, M., Zinterhof, P., Šilc, J., Robič, B., Eds.; Institute Jožef Stefan: Ljubljana, Slovenia, 1996; pp 17-27 (ISBN 86-80023-25-6).
    • (1996) Proceedings of the International Workshop PARALLEL NUMERICS '96 , pp. 17-27
    • Janežič, D.1    Merzel, F.2
  • 21
    • 5244323531 scopus 로고    scopus 로고
    • Simulations of Macromolecules: Improvements of MD Efficiency
    • Janežič, D.; Merzel, F. Simulations of Macromolecules: Improvements of MD Efficiency. Prog. Biophys. Mol. Biol. 1996, 65 (Sl), 48.
    • (1996) Prog. Biophys. Mol. Biol. , vol.65 , Issue.SL , pp. 48
    • Janežič, D.1    Merzel, F.2
  • 23
    • 84962423407 scopus 로고
    • Charge Populations of and Water Binding at the Oxygen Atoms of Some Esters
    • Koller, J.; Merzel, F.; Hadži, D. Charge Populations of and Water Binding at the Oxygen Atoms of Some Esters. J. Mol. Struct. 1993, 300, 233-238.
    • (1993) J. Mol. Struct. , vol.300 , pp. 233-238
    • Koller, J.1    Merzel, F.2    Hadži, D.3
  • 25
    • 84971897259 scopus 로고
    • Symplectic Integrators for Hamiltonian Problems: An Overview
    • Sanz-Serna, J. M. Symplectic Integrators for Hamiltonian Problems: An Overview. Acta Numerica 1991, 243-286.
    • (1991) Acta Numerica , pp. 243-286
    • Sanz-Serna, J.M.1
  • 28
    • 0040114714 scopus 로고
    • Recent Progress in the Theory and Application of Symplectic Integrators
    • Yoshida, H. Recent Progress in the Theory and Application of Symplectic Integrators. Celestial Mechanics and Dynamical Astronomy 1993, 56, 27-43.
    • (1993) Celestial Mechanics and Dynamical Astronomy , vol.56 , pp. 27-43
    • Yoshida, H.1
  • 29
    • 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
  • 30
    • 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
  • 31
    • 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
  • 32
    • 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
  • 33
    • 0343015666 scopus 로고    scopus 로고
    • Using Threads for Developing Parallel Applications: Molecular Dynamics as a Case Study
    • Trobec, R., Vajteršič, M., Zinterhof, P., Šilc, J., Robič, B., Eds.; Institute Jožef Stefan: Ljubljana, Slovenia, (ISBN 86-80023-25-6)
    • Bernard, E. P.; Plateau, B.; Trystram, D. Using Threads for Developing Parallel Applications: Molecular Dynamics as a Case Study. In Proceedings of the International Workshop PARALLEL NUMERICS '96; Trobec, R., Vajteršič, M., Zinterhof, P., Šilc, J., Robič, B., Eds.; Institute Jožef Stefan: Ljubljana, Slovenia, 1996; pp 3-16 (ISBN 86-80023-25-6).
    • (1996) Proceedings of the International Workshop PARALLEL NUMERICS '96 , pp. 3-16
    • Bernard, E.P.1    Plateau, B.2    Trystram, D.3
  • 34
    • 0001782767 scopus 로고
    • Parallelization of CHARMM for MIMD Machines
    • Brooks, B. R.; Hodošček, M. Parallelization of CHARMM for MIMD Machines. Chem. Des. Autom. News 1992, 7 (12), 16-22.
    • (1992) Chem. Des. Autom. News , vol.7 , Issue.12 , pp. 16-22
    • Brooks, B.R.1    Hodošček, M.2
  • 35
    • 84986534166 scopus 로고
    • New Spherical-Cutoff Methods for Long-Range Forces in Macromolecular Simulation
    • Steinbach, P. J.; Brooks, B. R. New Spherical-Cutoff Methods for Long-Range Forces in Macromolecular Simulation. J. Comput. Chem. 1994, 15, 667-683.
    • (1994) J. Comput. Chem. , vol.15 , pp. 667-683
    • Steinbach, P.J.1    Brooks, B.R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.