The MARTINI force field : Coarse grained model for biomolecular simulations
TLDR
An improved and extended version of the coarse grained lipid model is presented, coined the MARTINI force field, based on the reproduction of partitioning free energies between polar and apolar phases of a large number of chemical compounds to reproduce the free energies of these chemical building blocks.Abstract:
We present an improved and extended version of our coarse grained lipid model. The new version, coined the MARTINI force field, is parametrized in a systematic way, based on the reproduction of partitioning free energies between polar and apolar phases of a large number of chemical compounds. To reproduce the free energies of these chemical building blocks, the number of possible interaction levels of the coarse-grained sites has increased compared to those of the previous model. Application of the new model to lipid bilayers shows an improved behavior in terms of the stress profile across the bilayer and the tendency to form pores. An extension of the force field now also allows the simulation of planar (ring) compounds, including sterols. Application to a bilayer/cholesterol system at various concentrations shows the typical cholesterol condensation effect similar to that observed in all atom representations.read more
Citations
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Hybrid Approaches to Coarse-Graining using the VOTCA Package: Liquid Hexane
Victor Rühle,Christoph Junghans +1 more
TL;DR: Three hybrid schemes to combine force-matching and Boltzmann inversion are presented and all approaches can easily be extended to mixtures of molecules and provide insight for parametrizing building blocks of bigger molecules.
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Sustainable Nanotechnology: Opportunities and Challenges for Theoretical/Computational Studies.
Qiang Cui,Rigoberto Hernandez,Sara E. Mason,Thomas Frauenheim,Joel A. Pedersen,Franz M. Geiger +5 more
TL;DR: In this article, the authors highlight opportunities and pressing challenges for theoretical and computational chemistry approaches to explore the relevant physicochemical processes that span broad length and time scales, focusing on a bottom-up framework that relies on the determination of correct intermolecular forces, accurate molecular dynamics, and coarse-graining procedures to systematically bridge the scales, although top-down approaches are also effective at providing insights for many problems such as the effects of nanoparticles on biological problems.
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Comparing simulations of lipid bilayers to scattering data: the GROMOS 43A1-S3 force field.
TL;DR: Simulations of DOPC were performed using the united atom force field 43A1-S3 at six fixed projected areas and nonsimulation modeling obtains better simultaneous fits to both kinds of scattering data, which suggests that the force fields can still be improved.
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Topology, length scales, and energetics of surfactant micelles
TL;DR: An algorithm is developed to track micelle contours and quantify various microstructural features such as contour length distribution, persistence length, and mesh size, and predicts reliably the end-cap energy and recombination time of micelles, directly from molecular simulations for the first time.
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Understanding the curvature effect of silica nanoparticles on lysozyme adsorption orientation and conformation: a mesoscopic coarse-grained simulation study
TL;DR: This work simulated lysozyme adsorption on different-sized silica nanoparticles (SNPs) was simulated at the microsecond timescale by using mesoscopic coarse-grained molecular dynamics simulations to shed some light on how to prepare protein coronas with higher bioactivities in nanobiotechnology.
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