SCALE-MS workshop material

The git repository for this content is hosted at https://github.com/SCALE-MS/workshop

Workshop material includes content originally presented through https://github.com/kassonlab/gmxapi-tutorials, derived from the example in Figure 1 of 10.1371/journal.pcbi.1009835

Repository Contents

Sample inputs

Sample input files for these examples have been shared from previous research projects. They are covered by separate copyright and licensing details.

BRER workflow sample inputs: DOI 10.5281/zenodo.5122931

FS peptide (input_files/fs-peptide/): Sorin and Pande, Biophys J. 2005 Apr; 88(4): 2472–2493; doi:10.1529/biophysj.104.051938 (used with permission).

Getting started

• Install the required software.
• Get the sample input files.
• Clone this repository or pull a Docker image.

Install the software

Get the gmxapi 2022 software stack

• GROMACS 2022: https://gitlab.com/gromacs/gromacs/-/archive/release-2022/gromacs-release-2022.tar.gz
• gmxapi 0.3: use pip install gmxapi after installing and activating GROMACS 2022

Refer to installation instructions at the respective project websites.

• gmxapi on GROMACS,
• SCALE-MS Python package

Note that scalems depends on RADICAL Pilot. If you use pip to install scalems, radical.pilot and its dependencies will be installed automatically. Refer to https://scale-ms.readthedocs.io/en/latest/install.html for more information.

Alternative: Docker

If you prefer to use a containerized installation of the software and examples, and you are comfortable with Docker, see the docker directory in this repository or pull scalems/example-complete from DockerHub.

Accessing the tutorial material

From a local Python virtual environment

First, install GROMACS 2022, create a Python virtual environment, and install the gmxapi Python package (see above))

0. Clone this repository.

   git clone --recurse-submodules https://github.com/SCALE-MS/workshop.git
   cd workshop

1. Install additional tutorial dependencies in the virtual environment, using the provided requirements.txt.

   . /path/to/venv/bin/activate
   . /path/to/gromacs/bin/GMXRC
   pip install gmxapi
   pip install -r external/scale-ms/requirements-testing.txt
   pip install external/scale-ms
   pip install -r requirements.txt

2. Install the support package for the workshop.

   pip install .

3. Refer to the scripts in examples/

From Docker

If you have Docker installed, you can build an image from the included Dockerfile or docker pull scalems/example-complete.

See docker/README.md for more information.

Docker notes

Warning: The --rm in the command line above tells Docker to remove the container when you shut down the container. Any edits you make to the notebook will be lost. If you want to save your changes, the best choice is to use the File->Download option from within the notebook. Alternatively, you could explicitly make a snapshot of the container with docker commit. You could run docker without the --rm option, but you will need to clean up extra containers manually to keep from filling up your hard disk.

Caveats (TODOs)

Workflow is not checkpointed. You are advised to use a clean working directory for each script invocation.