Multiple pathways in conformational transitions of the alanine dipeptide: An Application of dynamic importance sampling

Hyunbum Jang, Thomas B. Woolf

Research output: Contribution to journalArticle

Abstract

We present multiple dynamic transition pathways on the two-dimensional dihedral plane between conformational states of the alanine dipeptide. The method used in this study is dynamic importance sampling (DIMS). To perform DIMS, unbiased molecular dynamic simulations are used to generate equilibrium ensembles for the alanine dipeptide within different states. Free energy surfaces on the dihedral plane are calculated from the equilibrium simulations, and four energy minima defined from the surface are used as the starting and ending points for DIMS dynamics. The DIMS method represents an important step towards finding multiple transition pathways within complex biomolecular systems.

Original languageEnglish (US)
Pages (from-to)1136-1141
Number of pages6
JournalJournal of Computational Chemistry
Volume27
Issue number11
DOIs
StatePublished - Aug 1 2006

Keywords

  • Alanine dipeptide
  • CHARMM
  • Conformational transition
  • Dynamic importance sampling
  • Multiple pathways

ASJC Scopus subject areas

  • Chemistry(all)
  • Computational Mathematics

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