Fast-loading cached binder: 
This repository hosts published tutorials for performing molecular dynamics simulation of a small protein in water solution in GROMACS.
- Click on one of the above "launch binder" buttons and wait for a server to be provisioned.
- Enjoy learning with the tutorial!
If you want to use the Jupyter notebook outside of a binder, see the usage instructions found at https://gitlab.com/gromacs/online-tutorials/website.
Contributions are welcome. Please open an issue on GitLab to discuss, or make a pull request.
Changes are made via GitLab branches from which merge requests are made to the main branch.
Review of the work in progress is integral, and [GitLab CI][ci] builds binder images corresponding to the branch.
These can be accessed from the GitLab Container Registry for this project at https://gitlab.com/gromacs/online-tutorials/umbrella-sampling/container_registry/1697718.
Alternatively, follow the links from the README.md file for the branch.
Once reviewed, the changes in the merge request are submitted and the updated binder images built.
Because this workflow uses Docker, we need to ensure that the GitLab Runner that runs it enables Docker support. That is available in the general-usage shared GitLab Runner supplied by GitLab, but is not available in the GitLab Runner supplied by the tcblab Kubernetes cluster to the top-level gromacs group. So if CI pipelines fail because Docker is unavailable, go to Settings -> CI/CD -> Runners and make sure that shared runners are enabled and group runners are disabled.
The tutorial content is maintained as a Jupyter notebook running Python.
Its Python dependencies are expressed in the environment.yml file.
We want the notebook to run by itself and also as a binder.
When run by itself, the environment.yml file is enough to build a conda environment that can run it.
Instructions for users to do that are provided by the webpages built from https://gitlab.com/gromacs/online-tutorials/website.
When run as a binder, both we and mybinder.org use repo2docker to convert the contents of a repository checkout to a container.
We support the default mode for mybinder.org, which is to build the container upon startup following the environment.yml file found in the default branch.
This can take several minutes or longer.
We also want to let binder users have fast startup by providing mybinder.org with a pre-built container.
We can do this via the binder-cache branch, that contains just the necessary Dockerfile.
That Dockerfile pulls an image that is made automatically from the main branch by GitLab CI.
GitLab CI's .gitlab-ci.yml file calls repo2docker to build a container image like mybinder.org would do.
That image is pushed to the GitLab Container registry for this GitLab project: https://gitlab.com/gromacs/online-tutorials/umbrella-sampling/container_registry.
When the user clicks on the "fast-loading cached binder" link above, the Dockerfile in the binder-cache branch directs mybinder.org to pull the latest container image.
This provides the same content, but starts the binder faster.
See the LICENSE file.