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Multibody Molecular Dynamics I: Theoretical Development

[+] Author Affiliations
Rudranarayan M. Mukherjee, Kurt S. Anderson

Rensselaer Polytechnic Institute, Troy, NY

Paper No. DETC2007-35560, pp. 1473-1482; 10 pages
doi:10.1115/DETC2007-35560
From:
  • ASME 2007 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference
  • Volume 5: 6th International Conference on Multibody Systems, Nonlinear Dynamics, and Control, Parts A, B, and C
  • Las Vegas, Nevada, USA, September 4–7, 2007
  • Conference Sponsors: Design Engineering Division and Computers and Information in Engineering Division
  • ISBN: 0-7918-4806-X | eISBN: 0-7918-3806-4

abstract

This is the first paper in a series of two papers on using multibody dynamics algorithms and methods for coarse-grained molecular dynamics simulations. This paper presents the underlying framework for multi-scale modelling of biomolecules and polymers. In this framework, the system to be simulated is sub-structured into a hierarchy of multi-resolution models that are simulated using efficient multibody dynamics algorithms. The algorithms work in a unified framework, enabling efficient multi-scale (or multi-resolution) simulations. A discussion of the hierarchy of models with different resolutions along with the salient features of the appropriate multibody dynamics algorithms used for simulating them is presented. The unified scheme and the qualitative advantages of the method are discussed. Important implementation details such as boundary conditions, temporal integration schemes, interaction force field calculations and solvent models are also presented. In the next paper applications and results are discussed.

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