https://github.com/ricalessandri/martini3-small-molecules

Martini 3 small-molecule database
https://github.com/ricalessandri/martini3-small-molecules

coarse-graining database martini3 molecular-dynamics small-molecules

Last synced: 7 days ago
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Martini 3 small-molecule database

• Host: GitHub
• URL: https://github.com/ricalessandri/martini3-small-molecules
• Owner: ricalessandri
• License: apache-2.0
• Created: 2021-07-18T08:41:05.000Z (over 3 years ago)
• Default Branch: main
• Last Pushed: 2024-08-21T20:54:24.000Z (5 months ago)
• Last Synced: 2025-01-10T12:53:31.158Z (14 days ago)
• Topics: coarse-graining, database, martini3, molecular-dynamics, small-molecules
• Language: Shell
• Homepage: https://doi.org/10.1002/adts.202100391
• Size: 27.9 MB
• Stars: 56
• Watchers: 3
• Forks: 11
• Open Issues: 18
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        

# Martini 3 small-molecule database

This GitHub repository contains a collection of Martini 3 models for small molecules.

If you use or wish to cite the Martini 3 small-molecule database, please refer to the following publication:

- R. Alessandri, J. Barnoud, A.S. Gertsen, I. Patmanidis, A.H. de Vries, P.C.T. Souza, S.J. Marrink.

  "Martini 3 Coarse-Grained Force Field: Small Molecules", *Adv. Theory Simul.* **2022**, *5*, 2100391 [(open-access)](https://doi.org/10.1002/adts.202100391).

 

Additional references should be cited for particular models. Please check the header of the model for details.

 

## Quick links



  Current itp collection of Martini 3 small molecule models





  Current lookup table of Martini 3 small molecule models





  Tutorial: Parametrizing a new small molecule with Martini 3





  Building block reference table to guide bead type choice





  Talk about Martini 3 small molecules at the Martini Workshop 2021

  (slides)



## Brief summary of repo content

This repo contains:

- Martini 3 small molecule models (and supporting files, e.g., atomistic-to-Martini mapping files):

  [models/](./models)

- Tutorials and reference material to build your own Martini 3 model: 

  [tutorials/](./tutorials)

- The procedures used to compute properties: 

  [procedures/](./procedures)

  

Please make sure to check the `README.md` in each subfolder for some more information and details. 

## Contributing

Contributions are welcome as [bug reports] and [pull requests] from everyone.

## License



Copyright 2021 University of Groningen


Licensed under the Apache License, Version 2.0 (the "License");

you may not use this file except in compliance with the License.

You may obtain a copy of the License at

        http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software

distributed under the License is distributed on an "AS IS" BASIS,

WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

See the License for the specific language governing permissions and

limitations under the License.



The [full text of the license](https://github.com/ricalessandri/Martini3-small-molecules/blob/master/LICENSE) 

is available in the source repository.

[bug reports]: https://github.com/ricalessandri/Martini3-small-molecules/issues

[pull requests]: https://github.com/ricalessandri/Martini3-small-molecules/pulls