ArticleThe journal of physical chemistry. B2013
Molecular dynamics simulations of DPPC bilayers using "LIME", a new coarse-grained model.
Article in The journal of physical chemistry. B, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Glutamate Permeability of Chicken Best1.Experimental neurobiology · 2022Article
- Development of a coarse-grained lipid model, LIME 2.0, for DSPE using multistate iterative Boltzmann inversion and discontinuous molecular dynamics simulations.Fluid phase equilibria · 2020Article
- Modelling lipid systems in fluid with Lattice Boltzmann Molecular Dynamics simulations and hydrodynamics.Scientific reports · 2019Article
- Computational Modeling of Realistic Cell Membranes.Chemical reviews · 2019Review
- A Discontinuous Potential Model for Protein-Protein Interactions.Foundations of Molecular Modeling and Simulation : select papers from FOMMS 2015. International Conference on Foundations of Molecular Modeling and Simulation (6th : 2015 : Mount Hood, Or.) · 2016Article
- Article
- Phase separation behavior of mixed lipid systems at neutral and low pH: coarse-grained simulations with DMD/LIME.Langmuir : the ACS journal of surfaces and colloids · 2015Article
- Transferring the PRIMO Coarse-Grained Force Field to the Membrane Environment: Simulations of Membrane Proteins and Helix-Helix Association.Journal of chemical theory and computation · 2014Article
- The power of coarse graining in biomolecular simulations.Wiley interdisciplinary reviews. Computational molecular science · 2014Article
- Proximal distributions from angular correlations: a measure of the onset of coarse-graining.The Journal of chemical physics · 2013Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
A new intermediate resolution model for phospholipids, LIME, designed for use with discontinuous molecular dynamics (DMD) simulations is presented. The implicit-solvent model was developed using a multiscale modeling approach in which the geometric and energetic parameters are obtained by collecting data from atomistic simulations of a system composed of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) molecules and explicit water. In the model, 14 coarse-grained sites that are classified as 1 of 6 types represent DPPC. DMD simulations performed on a random solution of DPPC resulted in the formation of a defect-free bilayer in less than 4 h. The bilayer formed quantitatively reproduces the main structural properties (e.g., area per lipid, bilayer thickness, bond order parameters) that are observed experimentally. In addition, the bilayer transitions from a liquid-crystalline phase to a tilted gel phase when the temperature is reduced. Transbilayer movement of a lipid from the bottom leaflet to the top leaflet is observed when the temperature is increased.
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