0

Full Content is available to subscribers

Subscribe/Learn More  >

An Efficient O(N) Algorithm for Computer Simulation of Rigid Body Molecular Dynamics

[+] Author Affiliations
Shanzhong Duan, Andrew Ries

South Dakota State University, Brookings, SD

Paper No. IMECE2007-42032, pp. 49-55; 7 pages
doi:10.1115/IMECE2007-42032
From:
  • ASME 2007 International Mechanical Engineering Congress and Exposition
  • Volume 12: New Developments in Simulation Methods and Software for Engineering Applications
  • Seattle, Washington, USA, November 11–15, 2007
  • Conference Sponsors: ASME
  • ISBN: 0-7918-4306-8 | eISBN: 0-7918-3812-9
  • Copyright © 2007 by ASME

abstract

Molecular dynamics is effective for a nano-scale phenomenon analysis. There are two major computational costs associated with computer simulation of atomistic molecular dynamics. They are calculation of the interaction forces and formation/solution of equations of motion. In this paper, an O(N) (order N) procedure is presented for calculation of the interaction forces and formation/solution of equations of motion. For computational costs associated with potentials or interaction forces, an internal coordinate method is used. Use of the internal coordinate method makes application of multi-rigid body molecular dynamics to an atomistic molecular system become possible. The algorithm based on the method makes the calculation considerably more practical for large-scale problems encountered in molecular dynamics such as conformation dynamics of polymers. For computational costs associated with formation/solution of equations of motion, Kane method and the internal coordinate method are used for recursive formation and solution of equations of motion of an atomistic molecular system. However, in computer simulation of atomistic molecular dynamics, the inclusion of lightly excited all degrees of freedom of an atom, such as inter-atomic oscillations and rotation about double bonds with high frequencies, introduces limitations to the simulation. The high frequencies of these degrees of freedom force the use of very small integration step sizes, which severely limit the time scales for the atomic molecular simulation over long periods of time. To improve this, holonomic constraints such as strictly constant bond lengths and bond angles are introduced to freeze these high frequency degrees of freedom since they have insignificant effect on long time scale processes in conformational dynamics. In this way, the procedure developed in multibody dynamics can be utilized to achieve higher computing efficiency and an O(N) computational performance can be realized for formation/solution of equations of motion.

Copyright © 2007 by ASME

Figures

Tables

Interactive Graphics

Video

Country-Specific Mortality and Growth Failure in Infancy and Yound Children and Association With Material Stature

Use interactive graphics and maps to view and sort country-specific infant and early dhildhood mortality and growth failure data and their association with maternal

NOTE:
Citing articles are presented as examples only. In non-demo SCM6 implementation, integration with CrossRef’s "Cited By" API will populate this tab (http://www.crossref.org/citedby.html).

Some tools below are only available to our subscribers or users with an online account.

Related Content

Customize your page view by dragging and repositioning the boxes below.

Related eBook Content
Topic Collections

Sorry! You do not have access to this content. For assistance or to subscribe, please contact us:

  • TELEPHONE: 1-800-843-2763 (Toll-free in the USA)
  • EMAIL: asmedigitalcollection@asme.org
Sign In