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kassonlab / gmxapi

(outdated) fork of https://gitlab.com/gromacs/gromacs
http://gmxapi.org/
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Tutorial / working Jupyter notebook examples #30

Open eirrgang opened 6 years ago

eirrgang commented 6 years ago

Task for #27

We need a quick-start sample workflow to help new users understand what gmxapi does and to experience it hands-on. The current restrained ensemble system requires far too much CPU time to be an effective introduction.

We need a sufficiently small biological molecule that we can sample the conformation of, set a target distribution of some conformation data, and then apply the ensemble restraint, demonstrating some amount of approach to convergence within a few minutes. @peterkasson suggests a molecule such as the funnel web spider toxin 1OMB.PDB used in the Kerrigan GROMACS 4.6 tutorial.

Ideally, the example / tutorial can be run interactively in a Jupyter notebook.

thavlik commented 4 years ago

Is this is still a work in progress? I built notebook.dockerfile and cannot import gmx, so I'm thinking that might be where you left off.

Thanks

eirrgang commented 4 years ago

Thanks for the note! This has been on the back burner, and it looks like the Jupyter example notebook for the sample_restraint is out of data for GROMACS 2020 (and gmxapi 0.1), though the release-0_0_7 branch should have some minimal examples for GROMACS 2019 and gmxapi 0.0.7.

The notebook you were looking at is probably the example that you can access in gmxapi/sample_restraint, which you can pull from DockerHub. It is not much of a tutorial, however.

See also https://github.com/kassonlab/sample_restraint/issues/44

Also, primary development and issue tracking has moved to the upstream GROMACS project. There is some housekeeping that needs to happen in this repository, though.