How to Install GROMACS 2024.3 on Linux, and Windows

10.02.26 11:05 AM - By Scientiflow

How to Install GROMACS 2024.3 on Linux, and Windows

GROMACS is a widely used molecular dynamics simulation software, vital for research in computational chemistry and biology. This guide provides step-by-step instructions to install the latest GROMACS version (2024.3) on different operating systems. For users facing installation challenges, we also introduce Singularity, a containerization alternative.

Installation on Linux:

Download GROMACS: Visit the official GROMACS download page and obtain the source code for version 2024.3.

Install Dependencies:

sudo apt update

sudo apt install cmake gcc g++ build-essential libfftw3-dev

Compile and Install:

tar xfz gromacs-2024.3.tar.gz

cd gromacs-2024.3

mkdir build && cd build

cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON

make -j$(nproc)

sudo make install

Activate GROMACS:

Add the following to your ~/.bashrc by running below command:

source /usr/local/gromacs/bin/GMXRC

Verify installation through below command:

gmx --version

If installation issues persist, consider using Singularity containerization technology as a fallback (see below).

Installation on Windows using WSL

Set Up WSL

The easiest way to install WSL is through the Microsoft Store:

Open Microsoft Store.
Search for Ubuntu.
Install your preferred version (e.g., Ubuntu 22.04.5 LTS).

Update and upgrade Ubuntu:

sudo apt update && sudo apt upgrade -y

Install GROMACS in WSL: Follow the same steps as in the Linux installation above.

Run GROMACS: Launch GROMACS from the WSL terminal like you would on Linux.

Why WSL?

Installing WSL makes it easy to run Linux applications without setting up a dual boot or virtual machine. It's an ideal solution for Windows users exploring computational research tools.

Using Singularity as a Backup Plan

If installing GROMACS directly is not feasible, you can use Singularity to run prebuilt containers. ScientiFlow maintains a GROMACS 2024.3 container for simplified usage.

Install Singularity

To install Singularity directly on your Linux environment or WSL enabled Windows, you might refer to official documentation of Singularity for the installation steps.

If you are encountering error or finding it difficult to install it from the official website, you can download the singularity_install.sh script from our Github:

Make it executable and run it with:

chmod +x singularity_install.sh

sudo ./singularity_install.sh

Pull the GROMACS container:

singularity pull gromacs.sif docker://scientiflow/gromacs:2024.3

Execute commands within the container:

singularity exec gromacs.sif gmx --version

Why Choose Singularity?

Singularity ensures consistency and eliminates dependency issues by packaging GROMACS and its environment into a container. This way, we can pull the container, and execute gromacs commands without requiring additional configuration steps. This approach is particularly useful when running GROMACS on systems with limited software compatibility.