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 to v2.6.1, we recommend to install one of these versions 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 python=3.11.0

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

Alternative Installation via Conda

The AiiDA-Gromacs plugin is also available via the CCPBioSim Anaconda channel.

To install using Conda:

conda activate aiida-2.4.0
conda install -c CCPBioSim aiida-gromacs

Or using mamba:

mamba install -c CCPBioSim 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, v23.4 and v24.2, 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-3.30.2-linux-x86_64.sh

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

export PATH="~/cmake-3.30.2-linux-x86_64.sh/bin:$PATH"

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

Full GROMACS Installation

The full GROMACS intallation may take some time (approximately 1 hour),

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

Limited GROMACS Installation

For a quicker, but limited GROMACS installation with OPENMP and MPI turned off, execute the following in the terminal:

tar xfz gromacs-2022.4.tar.gz
cd gromacs-2022.4
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
ccmake . # This will open a TUI, turn off OPENMP and THREAD_MPI, press 'c' to configure
make -j16 # This will compile GROMACS with 16 threads, change this to the number of threads you have available
sudo make install
source /usr/local/gromacs/bin/GMXRC

Add the GROMACS path to the .bashrc file:

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

To implement the changes to the .bashrc file, execute the following in the terminal:

source ~/.bashrc

Check GROMACS is available in the terminal with:

gmx -version

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