ArticleJournal of chemical theory and computation2017
Drude Polarizable Force Field for Molecular Dynamics Simulations of Saturated and Unsaturated Zwitterionic Lipids.
Article in Journal of chemical theory and computation, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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Who cites it
53 citing papers in PubMed.
- Investigating the electrostatics underlying activation of the βBiochimica et biophysica acta. Biomembranes · 2026Article
- Structural and Electronic Properties of Poly(ethylene terephthalate) (PET) from Polarizable Molecular Dynamics Simulations.Macromolecules · 2025Article
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- Statistical Mechanical Theories of Membrane Permeability.The journal of physical chemistry. B · 2024Article
- Effective Inclusion of Electronic Polarization Improves the Description of Electrostatic Interactions: The prosECCo75 Biomolecular Force Field.Journal of chemical theory and computation · 2024Article
- Quantifying Induced Dipole Effects in Small Molecule Permeation in a Model Phospholipid Bilayer.The journal of physical chemistry. B · 2024Article
- Evaluating Polarizable Biomembrane Simulations against Experiments.Journal of chemical theory and computation · 2024Article
- How is Membrane Permeation of Small Ionizable Molecules Affected by Protonation Kinetics?The journal of physical chemistry. B · 2024Article
- Drude Polarizable Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for Saturated and Monounsaturated Zwitterionic Lipids.Journal of chemical theory and computation · 2023Article
- Standard Binding Free Energy and Membrane Desorption Mechanism for a Phospholipase C.Journal of chemical information and modeling · 2022Article
- Charged Small Molecule Binding to Membranes in MD Simulations Evaluated against NMR Experiments.The journal of physical chemistry. B · 2022Article
- Extension of the CHARMM Classical Drude Polarizable Force Field to N- and O-Linked Glycopeptides and Glycoproteins.The journal of physical chemistry. B · 2022Article
- Accurate modeling of RNA hairpins through the explicit treatment of electronic polarizability with the classical Drude oscillator force field.Journal of computational biophysics and chemistry · 2022Article
- Harnessing Deep Learning for Optimization of Lennard-Jones Parameters for the Polarizable Classical Drude Oscillator Force Field.Journal of chemical theory and computation · 2022Article
- Ion permeation, selectivity, and electronic polarization in fluoride channels.Biophysical journal · 2022Article
- Accurate Simulations of Lipid Monolayers Require a Water Model with Correct Surface Tension.Journal of chemical theory and computation · 2022Article
- Influence of Charge Lipid Head Group Structures on Electric Double Layer Properties.Journal of chemical theory and computation · 2022Article
- Global Optimization of the Lennard-Jones Parameters for the Drude Polarizable Force Field.Journal of chemical theory and computation · 2021Article
- Molecular dynamics simulation study of the positioning and dynamics of α-tocopherol in phospholipid bilayers.European biophysics journal : EBJ · 2021Article
- Evaluation of log P, pKJournal of computer-aided molecular design · 2021Article
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6 authors.
Funding
Abstract
Additive force fields are designed to account for induced electronic polarization in a mean-field average way, using effective empirical fixed charges. The limitation of this approximation is cause for serious concerns, particularly in the case of lipid membranes, where the molecular environment undergoes dramatic variations over microscopic length scales. A polarizable force field based on the classical Drude oscillator offers a practical and computationally efficient framework for an improved representation of electrostatic interactions in molecular simulations. Building on the first-generation Drude polarizable force field for the dipalmitoylphosphatidylcholine 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) molecule, the present effort was undertaken to improve this initial model and expand the force field to a wider range of phospholipid molecules. New lipids parametrized include dimyristoylphosphatidylcholine (DMPC), dilauroylphosphatidylcholine (DLPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), dipalmitoylphosphatidylethanolamine (DPPE), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE), and 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE). The iterative optimization protocol employed in this effort led to lipid models that achieve a good balance between reproducing quantum mechanical data on model compound representative of phospholipids and reproducing a range of experimental condensed phase properties of bilayers. A parametrization strategy based on a restrained ensemble-maximum entropy methodology was used to help accurately match the experimental NMR order parameters in the polar headgroup region. All the parameters were developed to be compatible with the remainder of the Drude polarizable force field, which includes water, ions, proteins, DNA, and selected carbohydrates.
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