메뉴 건너뛰기




Volumn , Issue , 2003, Pages 167-171

Nonlinear instability in multiple time stepping molecular dynamics

Author keywords

Linear instability; Long molecular dynamics simulations; Multiple time stepping; Nonlinear instability; Verlet I r RESPA Impulse

Indexed keywords

COMPUTER SIMULATION; EQUATIONS OF MOTION; POTENTIAL ENERGY; RESONANCE; VECTORS;

EID: 0037999103     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/952532.952568     Document Type: Conference Paper
Times cited : (4)

References (21)
  • 1
    • 0001564321 scopus 로고
    • Dangers of multiple-time-step methods
    • Dec.
    • J. J. Biesiadecki and R. D. Skeel, Dangers of multiple-time-step methods. J. Comput. Phys., 109(2):318-328, Dec. 1993.
    • (1993) J. Comput. Phys. , vol.109 , Issue.2 , pp. 318-328
    • Biesiadecki, J.J.1    Skeel, R.D.2
  • 2
    • 0000316648 scopus 로고    scopus 로고
    • Difficulties with multiple timestepping and the fast multipole algorithm in molecular dynamics
    • Nov. 15
    • T. Bishop, R. D. Skeel, and K. Schulten. Difficulties with multiple timestepping and the fast multipole algorithm in molecular dynamics. J. Comp. Chem., 18(14):1785-1791, Nov. 15, 1997.
    • (1997) J. Comp. Chem. , vol.18 , Issue.14 , pp. 1785-1791
    • Bishop, T.1    Skeel, R.D.2    Schulten, K.3
  • 3
    • 0032226405 scopus 로고    scopus 로고
    • Long-time-step methods for oscillatory differential equations
    • Oct. 20
    • B. García-Archilla, J. M. Sanz-Serna, and R. D. Skeel. Long-time-step methods for oscillatory differential equations. SIAM J. Sci. Comput., 20(3):930-963, Oct. 20, 1998.
    • (1998) SIAM J. Sci. Comput. , vol.20 , Issue.3 , pp. 930-963
    • García-Archilla, B.1    Sanz-Serna, J.M.2    Skeel, R.D.3
  • 5
    • 84963146276 scopus 로고
    • Generalized Verlet algorithm for efficient molecular dynamics simulations with long-range interactions
    • H. Grubmüller, H. Heller, A. Windemuth, and K. Schulten. Generalized Verlet algorithm for efficient molecular dynamics simulations with long-range interactions. Molecular Simulation, 6:121-142, 1991.
    • (1991) Molecular Simulation , vol.6 , pp. 121-142
    • Grubmüller, H.1    Heller, H.2    Windemuth, A.3    Schulten, K.4
  • 6
    • 2442448609 scopus 로고    scopus 로고
    • Geometric Numerical Integration: Structure-Preserving Algorithms for Ordinary Differential Equations. Springer-Verlag, Berlin
    • E. Hairer, C. Lubich, and G. Wanner. Geometric Numerical Integration: Structure-Preserving Algorithms for Ordinary Differential Equations, volume 31 of Springer Series in Computational Mathematics. Springer-Verlag, Berlin, 2002.
    • (2002) Volume 31 of Springer Series in Computational Mathematics , vol.31
    • Hairer, E.1    Lubich, C.2    Wanner, G.3
  • 7
    • 0038663417 scopus 로고    scopus 로고
    • Overcoming instabilities in Verlet-I/r-RESPA with the mollified impulse method
    • T. Schlick and H. H. Gan, editors, Proceedings of 3rd International Workshop on Methods for Macromolecular Modeling. Springer-Verlag, Berlin, New York
    • J. A. Izaguirre, Q. Ma, T. Matthey, J. Willcock, T. Slabach, B. Moore, and G. Viamontes. Overcoming instabilities in Verlet-I/r-RESPA with the mollified impulse method. In T. Schlick and H. H. Gan, editors, Proceedings of 3rd International Workshop on Methods for Macromolecular Modeling, volume 24 of Lecture Notes in Computational Science and Engineering, pages 146-174. Springer-Verlag, Berlin, New York, 2002.
    • (2002) Volume 24 of Lecture Notes in Computational Science and Engineering , vol.24 , pp. 146-174
    • Izaguirre, J.A.1    Ma, Q.2    Matthey, T.3    Willcock, J.4    Slabach, T.5    Moore, B.6    Viamontes, G.7
  • 8
    • 0000921742 scopus 로고    scopus 로고
    • Longer time steps for molecular dynamics
    • May 15
    • J. A. Izaguirre, S. Reich, and R. D. Skeel. Longer time steps for molecular dynamics. J. Chem. Phys., 110(19):9853-9864, May 15, 1999.
    • (1999) J. Chem. Phys. , vol.110 , Issue.19 , pp. 9853-9864
    • Izaguirre, J.A.1    Reich, S.2    Skeel, R.D.3
  • 11
    • 0002105056 scopus 로고    scopus 로고
    • A reversible averaging integrator for multiple time-scale dynamcis
    • B. Leimkuhler and S. Reich. A reversible averaging integrator for multiple time-scale dynamcis. J. Comput. Phys., 171:95-114, 2001.
    • (2001) J. Comput. Phys. , vol.171 , pp. 95-114
    • Leimkuhler, B.1    Reich, S.2
  • 12
    • 0037649247 scopus 로고    scopus 로고
    • Verlet-I/r-RESPA/Impulse is limited by nonlinear instability
    • Q. Ma, J. A. Izaguirre, and R. D. Skeel. Verlet-I/r-RESPA/Impulse is limited by nonlinear instability. Submitted to SIAM Journal on Scientific Computing. Preprint at http://www.nd.edu/̃qma1/pub/MaIS0x.pdf, 2001.
    • (2001) SIAM Journal on Scientific Computing
    • Ma, Q.1    Izaguirre, J.A.2    Skeel, R.D.3
  • 14
    • 0007148604 scopus 로고
    • Resonance in the dynamics of chemical systems simulated by the implicit midpoint scheme
    • M. Mandziuk and T. Schlick. Resonance in the dynamics of chemical systems simulated by the implicit midpoint scheme. Chem. Phys. Letters, 237:525-535, 1995.
    • (1995) Chem. Phys. Letters , vol.237 , pp. 525-535
    • Mandziuk, M.1    Schlick, T.2
  • 15
    • 0037987034 scopus 로고    scopus 로고
    • ProtoMol: A molecular dynamics framework with incremental parallelization
    • Proceedings in Applied Mathematics, Philadelphia, March. Society for Industrial and Applied Mathematics
    • T. Matthey and J. A. Izaguirre. ProtoMol: A molecular dynamics framework with incremental parallelization. In Proc. of the Tenth SIAM Conf. on Parallel Processing for Scientific Computing (PP01), Proceedings in Applied Mathematics, Philadelphia, March 2001. Society for Industrial and Applied Mathematics.
    • (2001) Proc. of the Tenth SIAM Conf. on Parallel Processing for Scientific Computing (PP01)
    • Matthey, T.1    Izaguirre, J.A.2
  • 16
    • 0037987027 scopus 로고
    • Stability of a numerical solution of differential equations
    • W. E. Milne and R. R. Reynolds. Stability of a numerical solution of differential equations. J. ACM, 6(2):196-203, 1959.
    • (1959) J. ACM , vol.6 , Issue.2 , pp. 196-203
    • Milne, W.E.1    Reynolds, R.R.2
  • 17
    • 0042694406 scopus 로고    scopus 로고
    • Nonlinear stability analysis of area-preserving integrators
    • June 20
    • R. D. Skeel and K. Srinivas. Nonlinear stability analysis of area-preserving integrators. SIAM J. Numer. Anal., 38(1):129-148, June 20, 2000.
    • (2000) SIAM J. Numer. Anal. , vol.38 , Issue.1 , pp. 129-148
    • Skeel, R.D.1    Srinivas, K.2
  • 19
    • 0030621830 scopus 로고    scopus 로고
    • A family of symplectic integrators: Stability, accuracy, and molecular dynamics applications
    • Jan.
    • R. D. Skeel, G. Zhang, and T. Schlick. A family of symplectic integrators: stability, accuracy, and molecular dynamics applications. SIAM J. Sci. Comput., 18(1):203-222, Jan. 1997.
    • (1997) SIAM J. Sci. Comput. , vol.18 , Issue.1 , pp. 203-222
    • Skeel, R.D.1    Zhang, G.2    Schlick, T.3
  • 20
    • 33646650705 scopus 로고
    • Reversible multiple time scale molecular dynamics
    • M. Tuckerman, B. J. Berne, and G. J. Martyna. Reversible multiple time scale molecular dynamics. J. Chem. Phys., 97(3): 1990-2001, 1992.
    • (1992) J. Chem. Phys. , vol.97 , Issue.3 , pp. 1990-2001
    • Tuckerman, M.1    Berne, B.J.2    Martyna, G.J.3
  • 21
    • 84946450438 scopus 로고
    • Algorithms for macromolecular dynamics and constraint dynamics
    • W. F. van Gunsteren and H. J. C. Berendsen. Algorithms for macromolecular dynamics and constraint dynamics. Mol. Phys., 34(5): 1311-1327, 1977.
    • (1977) Mol. Phys. , vol.34 , Issue.5 , pp. 1311-1327
    • Van Gunsteren, W.F.1    Berendsen, H.J.C.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.