MD Simulation
How to install GROMACS on Apple M1 (MacOS)?

We have provided a few articles on GROMACS installation on Ubuntu. In this article, we are going to install GROMACS [1] on Mac OS.
Installing prerequisites
You will have to install cmake on your system before installing GROMACS. Open a terminal and paste the following command:
% brew install cmake
If you have not installed brew yet, then install it now by following the steps given here.
Downloading regressiontests
We will use wget to download the regression tests package. If you have not installed wget on your system then use the following command:
% brew install wget
You can also download it from here.
Change to the directory where you want to download the packages, let’s say, ‘Downloads’. Paste the following command in the terminal:
% cd Downloads/
% wget https://ftp.gromacs.org/regressiontests/regressiontests-2021.5.tar.gz
Downloading Gromacs
Paste the following command or download it from here:
% wget https://ftp.gromacs.org/gromacs/gromacs-2021.5.tar.gz
Installing Regressiontests
Now extract the downloaded package as shown below:
% tar xvzf regressiontests-2021.5.tar.gz
Installing Gromacs
Enter pwd in the terminal and note down the path. We will use it later. Now, extract the downloaded Gromacs package.
% tar xvzf gromacs-2021.5.tar.gz
Move inside the gromacs directory.
% cd gromacs-2021.5/
Now make a new directory namely, build.
% mkdir build
Move inside the build directory and install gromacs.
% cd build/
% source cmake.. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=OFF -DCMAKE_C_COMPILER=gcc -DREGRESSIONTEST_PATH=/your/pwd/path/
% sudo make check
% sudo make install
Now add it to your path as shown below.
% sudo nano /etc/paths
Add the following line at the end of the file.
/usr/local/gromacs/bin/GMXRC
Save and exit.
After the successful installation, you may check the version of your Gromacs with a command to make sure the installation is finished as expected.
% gmx pdb2gmx --version
It should display the usage. Now, you have successfully installed GROMACS on Mac OS.
References
- Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1, 19-25.
MD Simulation
How to take snapshots of structure at specific times in GROMACS?

It is important to see the behavior of protein during an MD simulation. This can be achieved by taking snapshots in the form of PDB format. In this article, we have provided a few commands that you can use to take snapshots of a complete system or protein during MD simulation. (more…)
MD Simulation
GROMACS: Uses & Applications

GROMACS stands for GROningen MAchine for Chemical Simulations [1]. It is a very popular and one of the most widely used open-source bioinformatics software. It is generally used for molecular dynamics simulation of macromolecules. In this article, we will explain its uses and applications in bioinformatics studies. (more…)
MD Simulation
Easy installation of GROMACS on Ubuntu 18.04 & 20.04

We have provided several articles on GROMACS [1] installation on Ubuntu including the easy installation method for GROMACS version 5.x.x. In this article, we will provide shell scripts to install the latest (2021 series) of GROMACS on Ubuntu 18.04 and 20.04. (more…)
grugru
September 25, 2022 at 7:36 am
Thanks to your article, I successfully installed gromacs on my macOS Catalina. But I modified or added few command lines.
brew install cmake
brew link cmake
brew link –overwrite cmake
cmake –version #3.7.2 → 3.24.2
cmake -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=OFF -DCMAKE_C_COMPILER=gcc -DREGRESSIONTEST_PATH=/path/path/gromacs/regressiontest