Gromacs workshop installation instructions
This page contains software installation instructions for Gromacs workshops. When relevant, separate instructions are given for Windows, MacOS and Linux systems.
- For the tutorial “Computing trajectories efficiently on GPUs” and the “QM/MM” part we will use an external cluster and instructions will be provided during the workshop.
- After you have gone through the installation steps below, please download the tutorial Jupyter notebook, run the notebook from terminal with
jupyter-notebook tutorial.ipynb, and execute all cells in the notebook to make sure you have everything installed correctly.
GROMACS and Python packages
Perparatory steps for Windows users
We strongly recommend to use (and install if necessary) the Windows Subsystem for Linux, WSL. Inside it you will need Python 3 and the conda Python environment manager. A useful guide to doing this is found at https://github.com/kapsakcj/win10-linux-conda-how-to. Once you have WSL and conda installed, make an environment for the GROMACS tutorials.
Installing miniconda
Install miniconda for Python 3 by following
| Linux | MacOS | Windows |
|---|---|---|
| https://docs.conda.io/en/latest/miniconda.html#linux-installers | https://docs.conda.io/en/latest/miniconda.html#macosx-installers | https://github.com/kapsakcj/win10-linux-conda-how-to |
After having installed conda
Make an environment for the GROMACS tutorials with:
conda install -c conda-forge ocl-icd-system
conda create --name gromacs-tutorials -c conda-forge -c bioconda gromacs=2020.5 matplotlib nglview notebook numpy requests pandas seaborn -c rdkit
For MaxOS, we will have to stick to the older gromacs=2019.1
Please use a separate environment for biobb (bio-building blocks)
(Optional) MPI-enabled GROMACS
The tutorial on replica-exchange MD simulations requires MPI-based GROMACS. Since we will not be running production MD simulations during the tutorial it is not necessary to install an MPI version, and we will be providing reference output files for non-MPI GROMACS as a backup. However, if you want to install MPI-based GROMACS on your own computer we provide here a general installation based on conda which should work on MacOS, Linux and WSL under Windows. If you already have compilers and an MPI library installed on your computer, you can skip the first section below or refer to the official installation instructions (https://manual.gromacs.org/documentation/current/install-guide/index.html).
Install compilers, OpenMPI and CMake
conda create --name mpi
conda activate mpi
conda install -c conda-forge compilers
conda install -c conda-forge openmpi
conda install -c conda-forge cmake
Download GROMACS 2020.5
wget http://ftp.gromacs.org/pub/gromacs/gromacs-2020.5.tar.gz
cd gromacs-2020.5
(or git clone https://gitlab.com/gromacs/gromacs.git; cd gromacs; git checkout v2020.5)
Compile GROMACS
mkdir build
cd build
cmake .. -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DGMX_MPI=ON -DGMX_DOUBLE=OFF -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
make
make check
sudo make install
source /usr/local/gromacs/bin/GMXRC
You will now hopefully be able to run gmx_mpi!
You can also compile an MPI version of GROMACS by following these steps in a terminal (click “New” and select “Terminal”):
cd $HOME
wget http://ftp.gromacs.org/pub/gromacs/gromacs-2020.5.tar.gz
tar zxf gromacs-2020.5.tar.gz
cd gromacs-2020.5
mkdir build
cd build
cmake .. -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DGMX_MPI=ON -DGMX_DOUBLE=OFF -DGMX_FFT_LIBRARY=fftpack
make
This procedure will install gmx_mpi into /home/jovyan/gromacs-2020.5/build/bin which you can use for MPI-enabled simulations.