Installation

This page goes through the steps for installing the required packages to use the GROMACS plugin for AiiDA.

Python Virtual Environment

We recommend setting up a Python virtual environment via Conda, which can be installed by downloading the relevant installer here. If you’re using Linux, install conda via the terminal with:

bash Miniconda3-latest-Linux-x86_64.sh

Then add the conda path to the bash environment by appending the following to your .bashrc file:

export PATH="~/miniconda3/bin:$PATH"

Options for AiiDA Installation

Our AiiDA plugin has been tested with AiiDA v2.4.0, we recommend to install this version of AiiDA in a conda environment. If you are using a linux OS, execute the following in the terminal, which installs AiiDA via an initial mamba installation

conda install -c conda-forge mamba
mamba create --name aiida-2.4.0 -c conda-forge aiida-core=2.4.0 aiida-core.services=2.4.0

Plugin Installation

To install the AiiDA-gromacs plugin, activate the conda environment created previously and install our plugin via Pip,

conda activate aiida-2.4.0
pip install aiida-gromacs

GROMACS Installation

If GROMACS is not already installed, here’s a quick installation guide. Our plugin has been tested with GROMACS v22.4 and v23.1 and we suggest installation of one of these versions. GROMACS requires the latest version of cmake, you can download the relevant cmake installer and install this via the terminal with:

bash cmake-3.27.2-linux-x86_64.sh

And include the path to cmake in the .bashrc file:

export PATH="~/make-3.27.2-linux-x86_64/bin:$PATH"

Download the relevant GROMACS installer and install via the quick and dirty method, summarised below

tar xfz gromacs-2022.4.tar.gz
cd gromacs-2022.4
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
make
make check
sudo make install
source /usr/local/gromacs/bin/GMXRC

Add the GROMACS path to the .bashrc file:

export PATH=/usr/local/gromacs/bin:$PATH

That is it. You have completed the installation steps to record simulation data provenance for GROMACS.