The neighbor list algorithm for a parallelepiped box in molecular dynamics simulations

Zhiwei Cui, Yi Sun, Jianmin Qu

Research output: Contribution to journalArticlepeer-review

9 Scopus citations

Abstract

In classic molecular dynamics (MD) simulations, the conventional Verlet table, cell linked list and many other techniques have been adopted to increase the computational efficiency. However, these methods are only applicable in cubic systems. In this work, the above techniques along with the metric-tensor method are extended to handle NP ensembles, so that MD simulations can be carried out under the most general loading conditions. In order to do so, a particular spatial Cartesian reference frame is proposed to determine the scaling matrix. Also, a combination method, taking the advantages of the improved Verlet table and cell linked list, is established to identify the neighbor atoms very quickly in a parallelepiped box. An example using Lennard-Jones potential is presented to verify the validity of the proposed algorithm.

Original languageEnglish
Pages (from-to)1463-1469
Number of pages7
JournalChinese Science Bulletin
Volume54
Issue number9
DOIs
StatePublished - May 2009

Keywords

  • Molecular dynamics simulations
  • Neighbor algorithm
  • Parallelepiped box

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