WIGGLE: A new constrained molecular dynamics algorithm in Cartesian coordinates

  • Authors:

  • Sang-Ho Lee;Kim Palmo;Samuel Krimm

  • Affiliations:

  • Biophysics Research Division and Department of Physics, The University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109, USA;Biophysics Research Division and Department of Physics, The University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109, USA;Biophysics Research Division and Department of Physics, The University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109, USA

  • Venue:
  • Journal of Computational Physics
  • Year:
  • 2005

Quantified Score

Hi-index 31.46

Visualization

Abstract

The theory of conventional constrained molecular dynamics (MD) simulations is reexamined based on a projection operator approach. A new algorithm, named WIGGLE, is presented for MD simulations with internal constraints. At each time step, the algorithm utilizes the constrained accelerations derived from velocity adjustments to satisfy the hidden constraints, and provides both initial and final constrained values that are almost an order of magnitude closer to the desired values than does RATTLE. Its performance is compared with those of RATTLE and SHAKE for an octane molecule. Also presented are a formalism to additionally constrain the angular momentum about the center of mass and an expression for the local energy drift during each integration time step.