Provide complete examples and tutorials

[jaimergp]

README.md and examples/ are not enough. We should add complete tutorials and proper documentation, as suggested by @ajasja in #9. This would be probably tackled when I start writing the manuscript for OMMProtocol, around February.

In the meantime, we can chat here and provide different systems and sources. For example, some tutorials could include:

OMMProtocol

• [ ] Absolute beginner: prepared PDB file compatible with standard forcefield.
• [ ] Intermediate: prepare dirty PDB with PDBFixer.
• [ ] Advanced: use ambertools to prepare Prmtop/Inpcrd and then come back to ommprotocol.

OMMAnalyze

• [ ] Just to showcase how to obtain quick plots using the output files from OMMProtocol.

[jaimergp]

Hello! Quick report.

The OMMProtocol manuscript is now submitted. As part of that effort, I wrote some accompanying documentation that is now published on http://ommprotocol.readthedocs.io. While proper tutorials are yet to be included, there are some tips for beginners.

Hope it helps!

(Pinging @ajasja)

[ajasja]

Thanks, I'll give it a try in the near future. (I had/have some problems running openMM itself).

Good luck with the manuscript!

[jaimergp]

Thanks! And one more thing, I forgot to mention that you can find some prepackaged installers in the releases section that might be helpful.