Performance of the general amber force field in modeling aqueous POPC membrane bilayers

Balázs Jójárt, T. Martinek

Research output: Contribution to journalArticle

94 Citations (Scopus)

Abstract

The aim of this work was to answer the question of whether the general amber force field (GAFF) is good enough to simulate fully hydrated POPC membrane bilayers. The test system contained 128 POPC and 2985 TIP3P water molecules. The equilibration was carried out in a nonarbitrary manner to reach the stable liquid-crystalline phase. The simulations were performed by using particle mesh Ewald electrostatics implemented in molecular dynamics packages Amber8 (NPT ensembles) and NAMD2 (NPγT ensembles). The computational results were assessed against the following experimental membrane properties: (i) area per lipid, (ii) area compressibility modulus, (iii) order parameter, (iv) gauche conformations per acyl chain, (v) lateral diffusion coefficients, (vi) electron density profile, and (vii) bound water at the lipid/water interface. The analyses revealed that the tested force field combination approximates the experimental values at an unexpectedly good level when the NPγT ensemble is applied with a surface tension of 60 mN m-1 per bilayer. It is concluded that the GAFF/TIP3P combination can be utilized for aqueous membrane bilayer simulations, as it provides acceptable accuracy for biomolecular modeling.

Original languageEnglish
Pages (from-to)2051-2058
Number of pages8
JournalJournal of Computational Chemistry
Volume28
Issue number12
DOIs
Publication statusPublished - Sep 2007

Fingerprint

Amber
Force Field
Ensemble
Membrane
Lipids
Membranes
Water
Modeling
Density Profile
Compressibility
Test System
Conformation
Surface Tension
Molecular Dynamics
Electrostatics
Order Parameter
Diffusion Coefficient
Carrier concentration
Surface tension
Conformations

Keywords

  • AMBER
  • GAFF
  • Lipid bilayer
  • Membrane simulation
  • POPC

ASJC Scopus subject areas

  • Chemistry(all)
  • Safety, Risk, Reliability and Quality

Cite this

Performance of the general amber force field in modeling aqueous POPC membrane bilayers. / Jójárt, Balázs; Martinek, T.

In: Journal of Computational Chemistry, Vol. 28, No. 12, 09.2007, p. 2051-2058.

Research output: Contribution to journalArticle

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