Open eirrgang opened 6 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
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.
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.