Abstract
Improvements in the CHARMM all-atom force field for atomic-level molecular simulations of lipids are reported. Substantial adjustments have been made to the Lennard-Jones (LJ) hydrocarbon and torsional parameters and to the partial atomic charges and torsional parameters of the phosphate moiety. These changes were motivated by a combination of unexpected simulation results and recent high-level ab initio quantum mechanical calculations. The parameter optimization procedure is described, and the resulting energy function validated by an 11 ns molecular dynamics simulation of a hydrated phospholipid bilayer. Of note is the influence of the hydrocarbon LJ parameters on the conformational properties of the aliphatic tails, emphasizing the importance of obtaining the proper balance between the bonded and nonbonded portions of the force field. Compatibility with the CHARMM all-atom parameter sets for proteins and nucleic acids has been maintained such that high quality simulations of biologically interesting membranes are possible. The complete force field is included as Supporting Information and is available from www.pharmacy.umaryland.edu/∼alex.
Keywords
Force field (fiction)Molecular dynamicsChemistryAtomic chargeAb initioComputational chemistryLipid bilayerNucleic acidChemical physicsPotential energyAtom (system on chip)MoleculeMembranePhysicsComputer scienceOrganic chemistryClassical mechanicsQuantum mechanics
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Publication Info
- Year
- 2000
- Type
- article
- Volume
- 104
- Issue
- 31
- Pages
- 7510-7515
- Citations
- 757
- Access
- Closed
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Cite This
Scott E. Feller,
Alexander D. MacKerell
(2000).
An Improved Empirical Potential Energy Function for Molecular Simulations of Phospholipids.
The Journal of Physical Chemistry B
, 104
(31)
, 7510-7515.
https://doi.org/10.1021/jp0007843
Identifiers
- DOI
- 10.1021/jp0007843