Lipid14: The Amber Lipid Force Field
Top Cited Papers
Open Access
- 30 January 2014
- journal article
- research article
- Published by American Chemical Society (ACS) in Journal of Chemical Theory and Computation
- Vol. 10 (2), 865-879
- https://doi.org/10.1021/ct4010307
Abstract
The AMBER lipid force field has been updated to create Lipid14, allowing tensionless simulation of a number of lipid types with the AMBER MD package. The modular nature of this force field allows numerous combinations of head and tail groups to create different lipid types, enabling the easy insertion of new lipid species. The Lennard-Jones and torsion parameters of both the head and tail groups have been revised and updated partial charges calculated. The force field has been validated by simulating bilayers of six different lipid types for a total of 0.5 μs each without applying a surface tension; with favorable comparison to experiment for properties such as area per lipid, volume per lipid, bilayer thickness, NMR order parameters, scattering data, and lipid lateral diffusion. As the derivation of this force field is consistent with the AMBER development philosophy, Lipid14 is compatible with the AMBER protein, nucleic acid, carbohydrate, and small molecule force fields.Keywords
Funding Information
- National Science Foundation (NSF-1047875)
- National Science Foundation (NSF-1148276)
- University of California (UC Lab 09-LR-06-117793)
This publication has 100 references indexed in Scilit:
- Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized BornJournal of Chemical Theory and Computation, 2012
- Enhanced Lipid Diffusion and Mixing in Accelerated Molecular DynamicsJournal of Chemical Theory and Computation, 2011
- Application of Molecular Dynamics Simulations in Molecular Property Prediction. 1. Density and Heat of VaporizationJournal of Chemical Theory and Computation, 2011
- Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid TypesThe Journal of Physical Chemistry B, 2010
- Comparing Membrane Simulations to Scattering Experiments: Introducing the SIMtoEXP SoftwareThe Journal of Membrane Biology, 2010
- Areas of Monounsaturated DiacylphosphatidylcholinesBiophysical Journal, 2009
- CHARMM-GUI Membrane Builder for Mixed Bilayers and Its Application to Yeast MembranesBiophysical Journal, 2009
- Comparison of multiple Amber force fields and development of improved protein backbone parametersProteins-Structure Function and Bioinformatics, 2006
- Development and testing of a general amber force fieldJournal of Computational Chemistry, 2004
- A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP modelThe Journal of Physical Chemistry, 1993