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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Estimating the entropy of liquids from atom–atom radial distribution functions: silica, beryllium fluoride and water
TL;DR: In this paper, the pair correlation entropy is demonstrated to be sufficiently accurate that the density-temperature regime of anomalous behaviour as well as the strength of the entropy anomaly can be predicted reliably for both ionic melts and different rigid-body pair potentials for water.
Journal ArticleDOI
Molecular Mechanism of Ionic-Liquid-Induced Membrane Disruption: Morphological Changes to Bilayers, Multilayers, and Vesicles
TL;DR: Using coarse-grained molecular dynamics simulations, the results suggest that ILs that can easily insert into the lipid bilayer without diffusing across or inducing lipid flip-flop can be more disruptive to a lipid biomembrane.
Journal ArticleDOI
The Surfactin-Like Lipopeptides From Bacillus spp.: Natural Biodiversity and Synthetic Biology for a Broader Application Range.
Ariane Théatre,Carolina Cano-Prieto,Marco Bartolini,Yoann Laurin,Magali Deleu,Joachim Niehren,Tarik Fida,Saïcha Gerbinet,Mohammad Alanjary,Marnix H. Medema,Angélique Léonard,Laurence Lins,Ana Arabolaza,Hugo Gramajo,Harald Gross,Philippe Jacques +15 more
TL;DR: The peptide moiety of the surfactin is synthesized using huge multienzymatic proteins called NonRibosomal Peptide Synthetases.
Book ChapterDOI
Coarse-grained modeling for macromolecular chemistry.
TL;DR: A short introduction to multiscale simulation approaches in macromolecular chemistry is given and the coarse-grained simulation models developed to drive a simple model from a more detailed one are reviewed.
Journal ArticleDOI
Investigation of phase transitions of saturated phosphocholine lipid bilayers via molecular dynamics simulations.
Pouyan Khakbaz,Jeffery B. Klauda +1 more
TL;DR: MD simulations provide evidence for the relevancy of the CHARMM36 lipid force field for structures and add to the understanding of the less-defined Pβ phase.
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