Application of combined Monte Carlo and molecular dynamics method to simulation of dipalmitoyl phosphatidylcholine lipid bilayer

S. W. Chiu, M. M. Clark, Eric Jakobsson, Shankar Subramaniam, H. Larry Scott

Research output: Contribution to journalArticlepeer-review

Abstract

We describe a new equilibration procedure for the atomic level simulation of a hydrated lipid bilayer. The procedure consists of alternating molecular dynamics trajectory calculations in a constant surface tension and temperature ensemble with configurational bias Monte Carlo moves to different regions of the configuration space of the bilayer, in a constant volume and temperature ensemble. The procedure is described in detail and is applied to a bilayer of 100 molecules of dipalmitoyl phosphatidylcholine (DPPC) and 3205 water molecules. We find that the hybrid simulation procedure enhances the equilibration of the bilayer as measured by the convergence of the area per molecule and the segmental order parameters, as compared with a simulation using only molecular dynamics (MD). Progress toward equilibration is almost three times as fast in CPU time, compared with a purely MD simulation. Equilibration is complete, as judged by the lack of energy drift in three separate 200-ps runs of continuous MD started from different initial states. Results of the simulation are presented and compared with experimental data and with other recent simulations of DPPC.

Original languageEnglish (US)
Pages (from-to)1153-1164
Number of pages12
JournalJournal of Computational Chemistry
Volume20
Issue number11
DOIs
StatePublished - Aug 1999

Keywords

  • Atomic level simulation
  • Configurational bias Monte Carlo
  • Model membrane
  • Molecular dynamics

ASJC Scopus subject areas

  • Chemistry(all)
  • Computational Mathematics

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