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Easy installation of GROMACS on Ubuntu 18.04 & 20.04

Dr. Muniba Faiza

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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.

If you are still looking to install an old version of GROMACS (5.x.x), please read this article. There you will find both elaborative as well as easy installation methods.

Preparing system

Press Ctrl+Alt+T and a terminal will open up. In the terminal, type:

$ sudo apt-get update

$ sudo apt-get upgrade

Downloading the script

We have created a new installer for you that will easily install the latest version of GROMACS (2021) on your system.

For Ubuntu 18.04

Download the script using the following command.

$ wget https://bioinformaticsreview.com/repository/gromacs-installer-2021-ubuntu18.04.sh

For Ubuntu 20.04

Download the script using the following command.

$ wget https://bioinformaticsreview.com/repository/gromacs-installer-2021-ubuntu20.04.sh

Installing GROMACS

If the installer doesn’t work for you, then proceed with the normal installation method mentioned in this article. You have to replace the old version with the new one. After downloading the appropriate script, proceed with the following steps.

  • Make the script executable
    $ chmod +x gromacs-installer-2021-ubuntu18.04.sh
    or
    $ chmod +x gromacs-installer-2021-ubuntu20.04.sh
  • start the installer
    $ ./gromacs-installer-2021-ubuntu18.04.sh
    or
    $ ./gromacs-installer-2021-ubuntu20.04.sh
  • If it shows an error stating “Permission denied“, then run the above commands with sudo as shown below:
    $ sudo ./gromacs-installer-2021-ubuntu18.04.sh
    or
    $ sudo ./gromacs-installer-2021-ubuntu20.04.sh

It will take a few minutes to finish the installation. After that, you can check for successful installation using the following command:

$ gmx pdb2gmx --version


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.

Further Reading

Installing Gromacs on Ubuntu for MD Simulation

Video tutorial: Installing GROMACS on Ubuntu

Tutorial: Molecular dynamics (MD) simulation using Gromacs

Tutorial: MD simulation output analysis of protein using GROMACS

Tutorial: MD Simulation of a Protein-Ligand Complex using GROMACS

 

 

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

MD Simulation

GROMACS: Uses & Applications

Dr. Muniba Faiza

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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…)

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MD Simulation

How to create an index file in GROMACS for MD simulation?

Dr. Muniba Faiza

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How to create an index file in GROMACS for MD simulation?

MD simulation is a tricky technique if you don’t understand what you are doing through various parameters and algorithms in GROMACS [1]. That may lead to several errors. In this article, we are going to create an index file for the protein groups in GROMACS to solve such errors. (more…)

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MD Simulation

How to generate topology of small molecules & ligands for MD Simulation?

Dr. Muniba Faiza

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generate topology of small molecules & ligands for MD simulation

Generating the topology of small molecules/ligands is an important step in molecular dynamics (MD) Simulation. We explained it in previous articles as part of MD simulation tutorials. In this article, we will explain how can you generate the topology of ligands for MD simulation of complex or small molecules only. (more…)

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