Molecular dynamics study of a lipid bilayer: Convergence, structure, and long-time dynamics

Wataru Shinoda, Nobuo Namiki, Susumu Okazaki

Research output: Contribution to journalArticlepeer-review

60 Citations (Scopus)

Abstract

Long time molecular dynamics simulations for the dipalmitoylphosphatidylcholine lipid bilayer in the liquid crystal phase could successfully be performed in the isothermal-isobaric ensemble using the Nosé-Parrinello-Rahman extended system method. Three independent 2 ns calculations show excellent convergence to the same equilibrium state of the system in about 0.5 ns. Various structural properties such as atomic distribution, order parameter, gauche fraction in the alkyl chains, and bent structure of the head group and sn-2chain were satisfactorily reproduced. Dynamic quantities such as trans-gauche transition were qualitatively in good correspondence to the experiment. The calculations presented a microscopic picture of the whole molecular conformations, including the finding that there is not a collective tilt in the bilayer. Some interesting dynamical observations concerning large structural fluctuations and pendulum motion of the alkyl chains were also made.

Original languageEnglish
Pages (from-to)5731-5743
Number of pages13
JournalJournal of Chemical Physics
Volume106
Issue number13
DOIs
Publication statusPublished - Apr 1 1997
Externally publishedYes

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

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