(Can be non-gromacs)
- GROMACS Tutorials by Justin Lemkul
- Bioinformatics With BB on YouTube
- Computational Chemistry Blog with numerous topics
- Wei-Tse Hsu's notes on advanced sampling
- LAMMPS
- LAMMPS documentation is pretty good, specifically the “howto”s are useful
- LAMMPS tutorials by Simon Gravelle
- LiveCoMS best practices articles
- [Best practices for learning molecular simulation] (https://livecomsjournal.org/index.php/livecoms/article/view/v1i1e5957)
- Principles of modern molecular simulation methods, lecture series by Scott Shell (UC Santa Barbara)
- Calculating effective diffusion coefficients from bootstrapping
- LiveCoMS article on "Best practices in computing transport properties"
- MDAnalysis has lots of common analysis tools.
- Practical PyMol for beginners provides an introduction on PyMol which allows individually coded analysis
- The RDKit Book and RDKit Cookbook: tools for cheminformatics, structure building, substructure search, etc.
- Open Force Field (OpenFF) resourcesP
- OpenFF cookbook: examples of how to set up systems
- OpenFF Interchange: for exporting your OpenFF systems to GROMACS, OpenMM, LAMMPS, etc
- Polymerist toolkit and examples: Tim Bernat (Shirts Group) tools for end-to-end MD system building, parameterization, and MD file setup for any linear multimeric organic polymer-like system (synthetic polymers, proteins, lipids, etc.)
- EspalomaCharge GitHub : easy-to-install GNN charge model for very quick partial charge assignment
- Also the accompanying paper for those interested in the nuts and bolts