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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GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers
Mark Abraham,Teemu Murtola,Roland Schulz,Roland Schulz,Szilárd Páll,Jeremy C. Smith,Jeremy C. Smith,Berk Hess,Erik Lindahl,Erik Lindahl +9 more
TL;DR: GROMACS is one of the most widely used open-source and free software codes in chemistry, used primarily for dynamical simulations of biomolecules, and provides a rich set of calculation types.
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Gromacs 4.5
Sander Pronk,Szilárd Páll,Szilárd Páll,Roland Schulz,Roland Schulz,Per Larsson,Pär Bjelkmar,Pär Bjelkmar,Rossen Apostolov,Rossen Apostolov,Michael R. Shirts,Jeremy C. Smith,Jeremy C. Smith,Peter M. Kasson,David van der Spoel,David van der Spoel,Berk Hess,Berk Hess,Erik Lindahl,Erik Lindahl,Erik Lindahl +20 more
TL;DR: A range of new simulation algorithms and features developed during the past 4 years are presented, leading up to the GROMACS 4.5 software package, which provides extremely high performance and cost efficiency for high-throughput as well as massively parallel simulations.
Journal ArticleDOI
The MARTINI Coarse-Grained Force Field: Extension to Proteins
Luca Monticelli,Senthil K. Kandasamy,Xavier Periole,Ronald G. Larson,D. Peter Tieleman,Siewert-Jan Marrink +5 more
TL;DR: A new CG model for proteins as an extension of the MARTINI force field is developed and effectively reproduces peptide-lipid interactions and the partitioning of amino acids and peptides in lipid bilayers.
Journal ArticleDOI
Oxidized arachidonic and adrenic PEs navigate cells to ferroptosis
Valerian E. Kagan,Gaowei Mao,Feng Qu,José Pedro Friedmann Angeli,Sebastian Doll,Claudette M. St. Croix,Haider H. Dar,Bing Liu,Vladimir A. Tyurin,Vladimir B. Ritov,Alexandr A. Kapralov,Andrew A. Amoscato,Jianfei Jiang,Tamil S. Anthonymuthu,Dariush Mohammadyani,Qin Yang,Bettina Proneth,Judith Klein-Seetharaman,Simon C. Watkins,Ivet Bahar,Joel S. Greenberger,Rama K. Mallampalli,Brent R. Stockwell,Yulia Y. Tyurina,Marcus Conrad,Hülya Bayır +25 more
TL;DR: It is discovered that ferroptosis involves a highly organized oxygenation center, wherein oxidation in endoplasmic-reticulum-associated compartments occurs on only one class of phospholipids (phosphatidylethanolamines (PEs) and is specific toward two fatty acyls-arachidonoyl (AA) and AdA (AdA).
Journal ArticleDOI
Improved Parameters for the Martini Coarse-Grained Protein Force Field
Djurre H. de Jong,Gurpreet Singh,W. F. Drew Bennett,Clement Arnarez,Tsjerk A. Wassenaar,Lars V. Schäfer,Xavier Periole,D. Peter Tieleman,Siewert J. Marrink +8 more
TL;DR: Improve some of the bonded terms in the Martini protein force field that lead to a more realistic length of α-helices and to improved numerical stability for polyalanine and glycine repeats.
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