Abstract
The Martini model is a coarse-grained force field allowing simulations of biomolecular systems as well as a range of materials, including different types of nanomaterials of technological interest. Recently, a new version of the force field (version 3) has been released, that includes new parameters for lipids, proteins, carbohydrates, and a number of small molecules, but not yet carbon nanomaterials. Here, we present new Martini models for three major types of carbon nanomaterials: fullerene, carbon nanotubes, and graphene. The new models were parameterized within the Martini 3 framework, and reproduce semi-quantitatively a range of properties for each material. In particular, the model of fullerene yields excellent solid-state properties and good properties in solution, including correct trends in partitioning between different solvents and realistic translocation across lipid membranes. The models of carbon nanotubes reproduce the atomistic behavior of nanotube porins spanning lipid bilayers. The model of graphene reproduces structural and elastic properties, as well as trends in experimental adsorption enthalpies of organic molecules. All new models can be used in large-scale simulations to study the interaction with the wide variety of molecules already available in the Martini 3 force field, including biomolecular and synthetic systems.
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Supporting Information
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The Supporting information file contains additional details on methods and additional results obtained on preliminary models.
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CNT-M3-maker
Description
Software that generates a Martini 3 model for an open carbon nanotube (CNT) for use with the Gromacs simulation package. It provides a structure file (.gro), a topology-include file (.itp) and a position-restraints file (.itp).
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M3-fullerene-maker
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Software that generates a Martini 3 model of Fullerene for running the molecular dynamics simulation with the Gromacs simulation package. The script outputs both the structure file (.gro) and a topology file (.itp).
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M3-graphene-maker
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Software that generates a Martini 3 model of both finite and infinite graphene sheet for running the molecular dynamics simulation with the Gromacs simulation package. The script outputs both the structure file (.gro) and a topology file (.itp).
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