Getting started guide
There is so much to say about molecular dynamics (MD) simulations that at the beginning it may seem a bit daunting. Below we list a few resources that may be useful to step into the world of MD.
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Some useful books and reviews
- Frenkel & Smit, Understanding Molecular Simulation, From Algorithms to Applications (2nd. Ed., 2001).
- Allen & Tildesley, Computer Simulation of Liquids (2nd. Ed., 2017). See the companion repository.
- Best Practices for Foundations in Molecular Simulations, Braun et al. Living J. Comp. Mol. Sci. (2019). DOI: 10.33011/livecoms.1.1.5957
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How to use the Gromacs software package
- Justin Lemkul's tutorials page: http://www.mdtutorials.com/
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Analysis packages:
- The MDtraj Python library: http://mdtraj.org
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Coarse grained models
- SMOG: This webtool allows for you to generate parameters to run coarse-grained simulations in Gromacs with the famous Clementi model.
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Visualization