UserGuide icon indicating copy to clipboard operation
UserGuide copied to clipboard

Add UserGuide documentation for `IMDReader`

Open amruthesht opened this issue 1 month ago • 5 comments

The following PR address Issue #427 and adds UserGuide documentation for the IMDReader via imd.rst and a tutorial/example simulation_imd.ipynb.

The template for the documentation followed is deatiled in the original Issue #427


📚 Documentation preview 📚: https://mdanalysisuserguide--430.org.readthedocs.build/en/430/

amruthesht avatar Oct 10 '25 08:10 amruthesht

Check out this pull request on  ReviewNB

See visual diffs & provide feedback on Jupyter Notebooks.


Powered by ReviewNB

@ljwoods2 could you also have a quick look please?

orbeckst avatar Oct 10 '25 16:10 orbeckst

RTD installation fails because 3.10 not supported by MDA anymore. (Raised #431 )

orbeckst avatar Oct 30 '25 23:10 orbeckst

@amruthesht a simple thing to address are the issues from pre-commit https://github.com/MDAnalysis/UserGuide/actions/runs/18957769421/job/54138651607?pr=430

orbeckst avatar Oct 30 '25 23:10 orbeckst

I'm still a bit confused by the indication:

MDAnalysis supports IMDv3 only, which uses the IMDv3 protocol to provide continuous, gap-free streaming and is implemented in modern versions of GROMACS

but I just tried it with GMX 2025.3 (I actually have a genuine use case), and I see:

Unknown left-hand 'IMD-version' in parameter file

and then I see: https://imdclient.readthedocs.io/en/stable/usage.html#gromacs

The IMDv3 protocol is currently not available as part of the official GROMACS release or source code repository. However, the feature is currently available for use in the imd-v3 branch of the forked repository

That's a pretty substantial distinction, both in convenience (I often pull in GMX binaries from conda-forge) and trust (reviewed/merged by GMX core devs). It looks like this issue is relevant: https://gitlab.com/gromacs/gromacs/-/issues/5311

tylerjereddy avatar Nov 04 '25 23:11 tylerjereddy