ArticlePloS one2011
The ELBA force field for coarse-grain modeling of lipid membranes.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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Who cites it
49 citing papers in PubMed.
- A tutorial for mesoscale computer simulations of lipid membranes: tether pulling, tubulation and fluctuations.Soft matter · 2025Review
- Review
- The analysis of neutron reflectivity from Langmuir monolayers of lipids using molecular dynamics simulations: the role of lipid area.Royal Society open science · 2025Article
- Exploring the Properties of Curved Lipid Membranes: Comparative Analysis of Atomistic and Coarse-Grained Force Fields.The journal of physical chemistry. B · 2024Article
- Evaluation of Essential Dynamics and Fixed-Length Coarse Graining for Multidomain Proteins.The journal of physical chemistry. B · 2024Article
- Coarse-Graining Waters: Unveiling The Effective Hydrophilicity/Hydrophobicity of Individual Protein Atoms and The Roles of Waters' Hydrogens.Journal of chemical theory and computation · 2023Article
- Anomalous Diffusion of Polyelectrolyte Segments on Supported Charged Lipid Bilayers.Entropy (Basel, Switzerland) · 2023Article
- A brief history of visualizing membrane systems in molecular dynamics simulations.Frontiers in bioinformatics · 2023Article
- Protocol for the development of coarse-grained structures for macromolecular simulation using GROMACS.PloS one · 2023Article
- Effect of Disulfide Bridge on the Binding of SARS-CoV-2 Fusion Peptide to Cell Membrane: A Coarse-Grained Study.ACS omega · 2022Article
- Applications of Molecular Dynamics Simulation in Protein Study.Membranes · 2022Review
- Specific interactions of peripheral membrane proteins with lipids: what can molecular simulations show us?Bioscience reports · 2022Article
- Polymyxin B1 within theBiophysical reviews · 2021Review
- The automated optimisation of a coarse-grained force field using free energy data.Physical chemistry chemical physics : PCCP · 2021Article
- Anisotropic Electrostatic Interactions in Coarse-Grained Water Models to Enhance the Accuracy and Speed-Up Factor of Mesoscopic Simulations.The journal of physical chemistry. B · 2021Article
- Automated Coarse-Grained Mapping Algorithm for the Martini Force Field and Benchmarks for Membrane-Water Partitioning.Journal of chemical theory and computation · 2021Article
- Coarse-Grained Molecular Dynamics Simulations of Membrane Proteins: A Practical Guide.Methods in molecular biology (Clifton, N.J.) · 2021Article
- CGMD Platform: Integrated Web Servers for the Preparation, Running, and Analysis of Coarse-Grained Molecular Dynamics Simulations.Molecules (Basel, Switzerland) · 2020Article
- Structural behavior of amphiphilic polyion complexes interacting with saturated lipid membranes investigated by coarse-grained molecular dynamic simulations.RSC advances · 2020Article
- Ligand-protein interactions in lysozyme investigated through a dual-resolution model.Proteins · 2020Article
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2 authors.
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Abstract
A new coarse-grain model for molecular dynamics simulation of lipid membranes is presented. Following a simple and conventional approach, lipid molecules are modeled by spherical sites, each representing a group of several atoms. In contrast to common coarse-grain methods, two original (interdependent) features are here adopted. First, the main electrostatics are modeled explicitly by charges and dipoles, which interact realistically through a relative dielectric constant of unity (ε(r) = 1). Second, water molecules are represented individually through a new parametrization of the simple Stockmayer potential for polar fluids; each water molecule is therefore described by a single spherical site embedded with a point dipole. The force field is shown to accurately reproduce the main physical properties of single-species phospholipid bilayers comprising dioleoylphosphatidylcholine (DOPC) and dioleoylphosphatidylethanolamine (DOPE) in the liquid crystal phase, as well as distearoylphosphatidylcholine (DSPC) in the liquid crystal and gel phases. Insights are presented into fundamental properties and phenomena that can be difficult or impossible to study with alternative computational or experimental methods. For example, we investigate the internal pressure distribution, dipole potential, lipid diffusion, and spontaneous self-assembly. Simulations lasting up to 1.5 microseconds were conducted for systems of different sizes (128, 512 and 1058 lipids); this also allowed us to identify size-dependent artifacts that are expected to affect membrane simulations in general. Future extensions and applications are discussed, particularly in relation to the methodology's inherent multiscale capabilities.
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