Jump to main content
Jump to site search

Issue 37, 2012
Previous Article Next Article

GAFFlipid: a General Amber Force Field for the accurate molecular dynamics simulation of phospholipid

Author affiliations

Abstract

Previous attempts to simulate phospholipid bilayers using the General Amber Force Field (GAFF) yielded many bilayer characteristics in agreement with experiment, however when using a tensionless NPT ensemble the bilayer is seen to compress to an undesirable extent resulting in low areas per lipid and high order parameters in comparison to experiment. In this work, the GAFF Lennard-Jones parameters for the simulation of acyl chains are corrected to allow the accurate and stable simulation of pure lipid bilayers. Lipid bilayers comprised of six phospholipid types were simulated for timescales approaching a quarter of a microsecond under tensionless constant pressure conditions using Graphics Processing Units. Structural properties including area per lipid, volume per lipid, bilayer thickness, order parameter and headgroup hydration show favourable agreement with available experimental values. Expanding the system size from 72 to 288 lipids and a more experimentally realistic 2 × 288 lipid bilayer stack induces little change in the observed properties. This preliminary work is intended for combination with the new AMBER Lipid11 modular force field as part of on-going attempts to create a modular phospholipid AMBER force field allowing tensionless NPT simulations of complex lipid bilayers.

Graphical abstract: GAFFlipid: a General Amber Force Field for the accurate molecular dynamics simulation of phospholipid

Back to tab navigation

Supplementary files

Publication details

The article was received on 30 Apr 2012, accepted on 20 Jul 2012 and first published on 07 Aug 2012


Article type: Paper
DOI: 10.1039/C2SM26007G
Citation: Soft Matter, 2012,8, 9617-9627
  •   Request permissions

    GAFFlipid: a General Amber Force Field for the accurate molecular dynamics simulation of phospholipid

    C. J. Dickson, L. Rosso, R. M. Betz, R. C. Walker and I. R. Gould, Soft Matter, 2012, 8, 9617
    DOI: 10.1039/C2SM26007G

Search articles by author

Spotlight

Advertisements