The Martini Model in Materials Science.
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TLDR
In this article, the main applications to date of the Martini model in materials science are highlighted, and a perspective for the future developments in this field is given, particularly in light of recent developments such as the new version of the model, Martini 3.Abstract:
The Martini model, a coarse-grained force field initially developed with biomolecular simulations in mind, has found an increasing number of applications in the field of soft materials science. The model's underlying building block principle does not pose restrictions on its application beyond biomolecular systems. Here, the main applications to date of the Martini model in materials science are highlighted, and a perspective for the future developments in this field is given, particularly in light of recent developments such as the new version of the model, Martini 3.read more
Citations
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Chemically specific coarse-graining of polymers: Methods and prospects
Satyen Dhamankar,Michael A. Webb +1 more
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Two decades of Martini: Better beads, broader scope
Siewert J. Marrink,Luca Monticelli,Manuel N. Melo,Riccardo Alessandri,D. Peter Tieleman,Paulo C. T. Souza +5 more
TL;DR: The Martini model as mentioned in this paper is a coarse-grained force field for molecular dynamics simulations, originally developed for lipid-based systems by the groups of Marrink and Tieleman, has over the years been extended as a community effort to the current level of a general-purpose force field.
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Polyply; a python suite for facilitating simulations of macromolecules and nanomaterials
Fabian Grünewald,Riccardo Alessandri,Peter C. Kroon,Luca Monticelli,Paulo C. T. Souza,Siewert J. Marrink +5 more
TL;DR: The polyply software suite as mentioned in this paper leverages a multi-scale graph matching algorithm designed to generate parameters quickly and for arbitrarily complex polymeric topologies, and a generic multiscale random walk protocol capable of setting up complex systems efficiently and independent of the target force-field or model resolution.
Journal ArticleDOI
Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems
Adam Liwo,Cezary Czaplewski,Adam K. Sieradzan,Agnieszka G. Lipska,Sergey A. Samsonov,Rajesh K. Murarka +5 more
TL;DR: In this article, the physical basis of coarse-grained molecular dynamics, the coarsegrained force fields, the equations of motion and the respective numerical integration algorithms, and selected practical applications are discussed.
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Nonconverged Constraints Cause Artificial Temperature Gradients in Lipid Bilayer Simulations
Sebastian Thallmair,Sebastian Thallmair,Matti Javanainen,Balázs Fábián,Hector Martinez-Seara,Siewert J. Marrink +5 more
TL;DR: In this paper, the authors show that a significant temperature difference between molecule types can artificially arise in CG MD simulations with the standard Martini simulation parameters in GROMACS, and demonstrate that the underlying reason for this behavior is the presence of highly constrained moieties, such as cholesterol.
References
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Functional Supramolecular Polymers
TL;DR: The specific features of supramolecular polymers that can lead to applications in a variety of fields are reviewed, including: materials—in which processability and self-healing properties are of interest; biomedicine— in which the concerns are dynamic functionality and biodegradability; and hierarchical assembly and electronic systems—with an interest in unidirectionality of charge flow.
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Machine learning for molecular and materials science.
TL;DR: A future in which the design, synthesis, characterization and application of molecules and materials is accelerated by artificial intelligence is envisaged.
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PLUMED 2: New feathers for an old bird
TL;DR: This work presents PLUMED 2 here—a complete rewrite of the code in an object-oriented programming language (C++), which introduces greater flexibility and greater modularity, which both extends its core capabilities and makes it far easier to add new methods and CVs.
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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
Coarse grained model for semiquantitative lipid simulations
TL;DR: In this article, a coarse-grained (CG) model for lipid and surfactant systems is presented, where only a small number of coarse grained atom types interact using a few discrete levels of interaction.