Connect with us

MD Simulation

How to install GROMACS on Apple M1 (MacOS)?

Published

on

Installing 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

  1. 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. SoftwareX1, 19-25.

Dr. Muniba is a Bioinformatician based in New Delhi, India. She has completed her PhD in Bioinformatics from South China University of Technology, Guangzhou, China. She has cutting edge knowledge of bioinformatics tools, algorithms, and drug designing. When she is not reading she is found enjoying with the family. Know more about Muniba

Advertisement
1 Comment

1 Comment

  1. 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

You must be logged in to post a comment Login

Leave a Reply

MD Simulation

How to take snapshots of structure at specific times in GROMACS?

Published

on

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…)

Continue Reading

MD Simulation

GROMACS: Uses & Applications

Published

on

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…)

Continue Reading

MD Simulation

Easy installation of GROMACS on Ubuntu 18.04 & 20.04

Published

on

Installing GROMACS on ubuntu

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…)

Continue Reading

LATEST ISSUE

ADVERT