Add MDAnalysis/NanoVer notebook for analysis of NanoVer recordings

IRL2 / nanover-server-py

https://irl2.github.io/nanover-docs/#

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Add MDAnalysis/NanoVer notebook for analysis of NanoVer recordings #226

Closed hjstroud closed 3 months ago

hjstroud commented 3 months ago

This PR adds a notebook that details how to extract data from an iMD simulation recorded using NanoVer using MDAnalysis, and highlights some of the benefits of recording trajectories using the inbuilt NanoVer functionality.

As ever, comments and suggestions are welcome!

hjstroud commented 3 months ago

Whilst making this notebook I noticed that the units of the system and user forces are not being converted properly from the NanoVer units (kJ/(mol.nm)) to the MDAnalysis units (kJ/(mol.A)). I have flagged this in Issue #227, and this will be fixed with PR #228.