Integration Methods for Molecular Dynamics

  • Benedict J. Leimkuhler
  • Sebastian Reich
  • Robert D. Skeel
Part of the The IMA Volumes in Mathematics and its Applications book series (IMA, volume 82)

Abstract

Classical molecular dynamics simulation of a macromolecule requires the use of an efficient time-stepping scheme that can faithfully approximate the dynamics over many thousands of timesteps. Because these problems are highly nonlinear, accurate approximation of a particular solution trajectory on meaningful time intervals is neither obtainable nor desired, but some restrictions, such as symplecticness, can be imposed on the discretization which tend to imply good long term behavior. The presence of a variety of types and strengths of interatom potentials in standard molecular models places severe restrictions on the timestep for numerical integration used in explicit integration schemes, so much recent research has concentrated on the search for alternatives that possess (1) proper dynamical properties, and (2) a relative insensitivity to the fastest components of the dynamics. We survey several recent approaches.

Key words

leapfrog method Verlet method symplectic method multiple-timestep methods symplectic integrator molecular dynamics simulation constrained dynamics SHAKE multiple time scales long-time integration 

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Copyright information

© Springer-Verlag New York, Inc. 1996

Authors and Affiliations

  • Benedict J. Leimkuhler
    • 1
  • Sebastian Reich
    • 2
  • Robert D. Skeel
    • 3
  1. 1.Department of MathematicsUniversity of KansasLawrenceUSA
  2. 2.Konrad-Zuse ZentrumBerlinGermany
  3. 3.Department of Computer ScienceUniversity of IllinoisUrbanaUSA

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