gromacs

Versions: [2021.1, 2021.2, 2021.3]

gromacs

Download        : docker pull ghcr.io/autamus/gromacs
Compressed Size : 66MB

Description

GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics package primarily designed for simulations of proteins, lipids and nucleic acids. It was originally developed in the Biophysical Chemistry department of University of Groningen, and is now maintained by contributors in universities and research centers across the world. GROMACS is one of the fastest and most popular software packages available and can run on CPUs as well as GPUs. It is free, open source released under the GNU General Public License. Starting from version 4.6, GROMACS is released under the GNU Lesser General Public License.

Usage

Pull (Download)

To download the latest version of gromacs run,

docker pull ghcr.io/autamus/gromacs:latest

or to download a specific version of gromacs run,

docker pull ghcr.io/autamus/gromacs:2021.1

Run

To run the container as an application run,

docker run --rm ghcr.io/autamus/gromacs gromacs --version

or to run the container in an interactive session run,

docker run -it --rm ghcr.io/autamus/gromacs bash

Mounting volumes between the container and your machine

To access files from your machine within the gromacs container you’ll have to mount them using the -v external/path:internal/path option.

For example,

docker run -v ~/Documents/Data:/Data ghcr.io/autamus/gromacs gromacs /Data/myData.csv

which will mount the ~/Documents/Data directory on your computer to the /Data directory within the container.

HPC

If you’re looking to use this container in an HPC environment we recommend using Singularity-HPC to use the container just as any other module on the cluster. Check out the SHPC gromacs container here.