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Jonathan Barnoud

As seen in: Nature, arXiv, Cell Press, eLife
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Articles

Martinize2 and Vermouth provide a unified framework for molecular topology generation

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By Peter Kroon, Jonathan Barnoud, Marco van Tilburg, Chris Brasnett
| eLife
eLife Assessment The authors present an important multi-scale computational platform, which aims to automate the workflow for coarse-grained simulations of biomolecules in the framework of the popular MARTINI model. The capability of the platform has been convincingly demonstrated by the application to a large number of proteins as well as macrocycles and polymers. This work will be of interest to both computational biophysicists and chemists.
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Martinize2 and Vermouth: Unified Framework for Topology Generation

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By van Tilburg, Fabian Grünewald, Jonathan Barnoud, Paulo C. T
| arXiv
[Submitted on 29 Nov 2022 ( v1 ), last revised 30 Jun 2023 (this version, v2)] Title:Martinize2 and Vermouth: Unified Framework for Topology Generation Download a PDF of the paper titled Martinize2 and Vermouth: Unified Framework for Topology Generation, by Peter C.
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Martini 3: a general purpose force field for coarse-grained molecular dynamics

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By Riccardo Alessandri, Jonathan Barnoud, Sebastian Thallmair, Ignacio Faustino
| Nature Verified
Abstract The coarse-grained Martini force field is widely used in biomolecular simulations. Here we present the refined model, Martini 3 (http://cgmartini.nl), with an improved interaction balance, new bead types and expanded ability to include specific interactions representing, for example, hydrogen bonding and electronic polarizability.
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