Gromacs

class Gromacs(data_dir: Path, output_dir: Path)

Bases: object

Runs GROMACS commands in a docker container.

Note you have to create a docker image of gromacs/gromacs. If you are running windows you need to install Docker Desktop first https://www.docker.com/products/docker-desktop/

You then download the DOCKERFILE details for GROMACS by typing the following commands in a terminal to use the canonical Gromacs container:

git clone https://github.com/bioexcel/gromacs-docker

And then build the image by typing: cd gromacs-docker docker build .

subsequent calls to “docker run –rm -it gromacs/gromacs” will use the image you just built and give you an interactive terminal, and delete the container when you exit.

run(gromacs_commands: list, output_file_name: str)

run_simulation(mdp_file: str, gro_file: str, top_file: str, tpr_file: str, block: bool = True)

Runs a GROMACS simulation using the given mdp, gro, and top files.

Parameters:

• mdp_file (str) – the name of the parameter file

• gro_file (str) – the name of the molecular structure file

• top_file (str) – the name of the topology file

• tpr_file (str) – the name of the portable binary run input file

• block (bool, optional) – if True, then wait until the simulation has finished, otherwise run in the background, defaults to True