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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Bayesian parametrization of coarse-grain dissipative dynamics models
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Solvent‐Responsive Behavior of Polymer‐Brush‐Modified Amphiphilic Gold Nanoparticles
Jiaqi Dong,Jian Zhou +1 more
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Nonequilibrium Processes in Polymer Membrane Formation: Theory and Experiment.
Marcus Müller,Volker Abetz +1 more
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Interfacial Tension and Surface Pressure of High Density Lipoprotein, Low Density Lipoprotein, and Related Lipid Droplets
O. H. Samuli Ollila,O. H. Samuli Ollila,Antti Lamberg,Maria Lehtivaara,Artturi Koivuniemi,Ilpo Vattulainen,Ilpo Vattulainen +6 more
TL;DR: The results suggest that the curvature dependence of interfacial tension becomes significant for particles with a radius of ∼5 nm, when the area per molecule in the surface region is <1.4 nm(2), and that HDL and LDL are kinetically trapped into a metastable state.
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Identifying and Tracking Defects in Dynamic Supramolecular Polymers.
Piero Gasparotto,Piero Gasparotto,Davide Bochicchio,Michele Ceriotti,Giovanni M. Pavan,Giovanni M. Pavan +5 more
TL;DR: The power of unsupervised machine learning techniques is demonstrated to systematically identify and compare defects in supramolecular polymer variants in different conditions, using as a benchmark 5Å-resolution coarse-grained molecular simulations of a family of supramolescular polymers.
References
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