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Multibody Molecular Dynamics II: Applications and Results

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

Rensselaer Polytechnic Institute, Troy, NY

Paul Crozier

Sandia National Laboratories, Albuquerque, NM

Paper No. DETC2007-35561, pp. 1483-1493; 11 pages
doi:10.1115/DETC2007-35561
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 second paper in a series of two papers on using multibody dynamics algorithms and methods for coarse grained molecular dynamics simulations. In the previous paper, the theoretical discussions on this topic have been presented. This paper presents results obtained from simulating several biomolecular and bulk materials using multibody dynamics algorithms. The systems studied include water boxes, alkane chains, alanine dipeptide and carboxyl terminal fragments of Calmodulin, Ribosomal, and Rhodopsin proteins. The atomistic representations of these systems include several thousand degrees of freedom and results of several nano-second simulations of these systems are presented. The stability and validity of the simulations are studied through conservation of energy, thermodynamics properties and conformational analysis. In these simulations, a speed up of an order of magnitude is realized for conservative error bounds. A discussion is presented on the open-source software developed to facilitate future research using multibody dynamics with molecular dynamics.

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