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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Thermodynamically reversible paths of the first fusion intermediate reveal an important role for membrane anchors of fusion proteins
TL;DR: It is demonstrated that the isolated transmembrane domains (TMDs) of fusion proteins such as SNARE molecules drastically lower the free energy of both the stalk barrier and metastable stalk, which is not trivially explained by molecular shape arguments.
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Transport and dielectric properties of water and the influence of coarse-graining: Comparing BMW, SPC/E, and TIP3P models
TL;DR: Carefully monitoring energy/temperature conservation is found to be a sufficient criterion for the reliable calculation of dynamical properties, by contrast, recommended criteria based on the ratio of fluctuations of total vs. kinetic energy are not sensitive enough.
Journal ArticleDOI
Maximum Entropy Optimized Force Field for Intrinsically Disordered Proteins.
Andrew P. Latham,Bin Zhang +1 more
TL;DR: A generic algorithm is presented to improve the accuracy of coarse-grained IDP models using a diverse set of experimental measurements and combines maximum entropy optimization and least squares regression to systematically adjust model parameters and improve the agreement between simulation and experiment.
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Free Energy Landscape of Lipid Interactions with Regulatory Binding Sites on the Transmembrane Domain of the EGF Receptor
TL;DR: In this article, coarse-grained simulations were performed to calculate free energy profiles for glycolipids and phospholipids interacting with modulatory sites on the transmembrane helix dimer of the EGF receptor within a lipid bilayer environment.
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A Solvent-Free Coarse Grain Model for Crystalline and Amorphous Cellulose Fibrils
TL;DR: A coarse grain model for molecular dynamics simulations of cellulose using distribution functions from fully atomistic MD simulations as target observables provides an accurate and constraint-free approach to derive CG models for cellulose with a wide range of crystallinity, suitable for incorporation into large-scale models of lignocellulosic biomass.
References
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