# Mirror_gromacs_introduction-to-molecular-dynamics-tutorial

**Repository Path**: regentsai/md-intro-tutorial

## Basic Information

- **Project Name**: Mirror_gromacs_introduction-to-molecular-dynamics-tutorial
- **Description**: gromacs对分子动力学模拟的介绍教程的相关数据镜像.
- **Primary Language**: Unknown
- **License**: CC-BY-4.0
- **Default Branch**: main
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2022-12-31
- **Last Updated**: 2022-12-31

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

Fast-loading cached binder: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gl/gromacs%2Fonline-tutorials%2Fmd-intro-tutorial/binder-cache?filepath=tutorial.ipynb)
Default binder: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gl/gromacs%2Fonline-tutorials%2Fmd-intro-tutorial/main?filepath=tutorial.ipynb)

# CI status

[![pipeline status](https://gitlab.com/gromacs/online-tutorials/md-intro-tutorial/badges/main/pipeline.svg)](https://gitlab.com/gromacs/online-tutorials/md-intro-tutorial/-/commits/main)

# Molecular Dynamics Introduction Tutorial

This repository hosts published tutorials for performing molecular dynamics
simulation of a small protein in water solution in GROMACS.

## Usage

1. Click on one of the above "launch binder" buttons and wait for a server to
   be provisioned.
2. 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.

## Contributing

Contributions are welcome.
Please open an issue on GitLab to discuss, or make a pull request.

## Making and testing changes

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.

![Workflow for updating the website](images/development workflow.png)

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.

## Project structure

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.

## License

See the LICENSE file.

[repo2docker]: https://repo2docker.readthedocs.io/en/latest/
[mybinder.org]: https://mybinder.org/