GROMACS  is one of the most popular software in bioinformatics for molecular dynamic (MD) studies of macromolecules. We have provided different tutorials regarding MD simulation using GROMACS including its installation on Ubuntu. In this article, we will install GROMACS with GPU acceleration.
For detailed instructions, read our previous article. If you want to install without GPU support, you can simply follow the steps mentioned in that article. In this tutorial, you will find some additional steps for GPU acceleration.
It is good practice to update your repository information and software packages before installing new programs. Open a terminal by pressing Ctrl+Alt+T and type:
$ sudo apt-get update
$ sudo apt-get upgrade
Downloading CUDA toolkit
It might be possible that you have already NVIDIA CUDA drivers installed on your system. Therefore, it’s better to first remove them and then install the latest drivers, otherwise, it will give you errors. Open a terminal and type the following commands:
$ sudo apt-get remove --purge cuda-* libcuda* nvidia*
$ sudo apt-get remove --purge cuda-drivers libcuda* cuda-runtime* cuda-8-0 cuda-demo*
$ sudo apt-get autoremove --purge nvidia* cuda-drivers libcuda* cuda-runtime* cuda-8-0 cuda-demo*
$ sudo apt-get remove --purge nvidia* cuda-drivers libcuda1-396 cuda-runtime-9-2 cuda-9.2 cuda-demo-suite-9-2 cuda
Now select the latest version of the CUDA toolkit according to your system from here. Download the local run file using the following command. The run file contains every essential component to be installed. Change to the directory where you want to download the installer.
$ cd Downloads/
$ wget https://developer.download.nvidia.com/compute/cuda/11.1.1/local_installers/cuda_11.1.1_455.32.00_linux.run
Installing CUDA toolkit
Since the CUDA toolkit is available for Ubuntu 16.04 onwards, therefore, make sure you have the compatible version of Ubuntu installed on your system. Now, copy & paste the following command to run the installer.
$ sudo sh cuda_11.1.1_455.32.00_linux.run
It will ask to create a password, enter, and confirm. It will take a few minutes to finish. After that, edit /etc/ld.so.conf file.
$ sudo gedit /etc/ld.so.conf
Now add the following path at the end of the file.
$ sudo ldconfig
Now install CUDA drivers. To avoid any error, don’t forget to write the last argument in the command (–override-driver-check).
$ sudo sh cuda_11.1.1_455.32.00_linux.run --silent --driver --override-driver-check
Updating NVIDIA drivers
It is necessary to update the NVIDIA drivers otherwise it will not recognize GPU during simulation even after configuration. Copy & paste the following commands.
$ sudo ubuntu-drivers autoinstall
$ sudo apt-get update
Installing prerequisites for GROMACS
- Install openmpi from the repository using the following command:
$ sudo apt-get install libopenmpi-dev
$ sudo apt-get install openmpi-bin
$ sudo apt-get install mpi4py
If you have already installed GROMACS, then skip to the next step.
- Get cmake before installing GROMACS. In the terminal, type:
$ sudo apt-get install -y cmake
After the installation finishes up, you can check the version of cmake by the following command:
$ cmake --version
If it displays the version, then it means everything is fine. Move on to the next step.
- The next requirement is build-essential. To install this, type the following command in the terminal:
$ sudo apt-get install -y build-essential
- Now, you need the FFTW3 library. Install it using the following command:
$ sudo apt-get install -y libfftw3-dev
- Now, install Doxygen
$ sudo apt-get install -y doxygen
It is better to download the regressiontests separately because most of the time it throws an error stating that “the location of the file has changed”. Copy and paste the following commands in your terminal:
$ cd Downloads/
$ wget http://gerrit.gromacs.org/download/regressiontests-2020.4.tar.gz
Now, extract the downloaded file,
$ tar xvzf regressiontests-2020.4.tar.gz
Download the latest release of GROMACS from here or use the following command:
$ wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-2020.4.tar.gz
First, get your pwd path using the following command:
Note down the displayed path, we will need it in later steps.
- Extract the downloaded archive file. Move into the directory where you have downloaded the package. Let’s say, Downloads.
$ cd Downloads/
$ tar xvzf gromacs-2020.4.tar.gz
- Now move inside the gromacs folder.
$ cd gromacs-2020.4/
- Create a directory called “build-gpu” where we will keep our compiled binaries.
$ mkdir build-gpu
- Move inside the build-gpu directory
$ cd build-gpu/
- Now, make gromacs using cmake.
$ sudo cmake .. -DGMX_BUILD_OWN_FFTW=OFF -DREGRESSIONTEST_DOWNLOAD=OFF -DMAKE_C_COMPILER=gcc -DGMX_GPU=ON -DGMX_MPI=OFF -DREGRESSIONTEST_PATH=/your/pwd/path/here/Downloads/regressiontests-2020.4
If everything goes well, the message in your terminal will say “Generating Done. Build files written… “. If not, make sure you have replaced the pwd path in command with the path of your home directory.
- Now, let’s check and make.
$ make check
$ sudo make install
- Move inside the unpacked regressiontests directory and execute the following command:
$ source /usr/local/gromacs/bin/GMXRC
After that, you can check for the successful installation of GROMACS with the following command:
$ gmx pdb2gmx --version
It will display the GPU version as well.
Enjoy the speedy simulation!
Energy minimization and equilibration of simple protein using NAMD & VMD.
Generating topology of molecule for AMBER forcefield for GROMACS.
How to visualize output plots of MD simulation (GROMACS)?
Visualizing plots of molecular dynamics simulation is easy once you have generated them. Previously, we provided a few articles on MD output analysis (check the Further Reading section). This article explains how you can easily visualize the plots generated from GROMACS output. (more…)
How to solve ‘Could NOT find CUDA: Found unsuitable version “10.1”‘ error during GROMACS installation?
Compiling GROMACS  with GPU can be trivial. Previously, we have provided a few articles on the same. In this article, we will solve an error frequently occurring during GROMACS installation.
How to calculate number of steps (nsteps) for MD simulation run?
While doing molecular dynamics (MD) simulation, it can be difficult to calculate the number of steps or nsteps for an MD run accurately. In this article, we will learn to calculate nsteps for an MD run. (more…)
How to install GROMACS on Apple M1 (MacOS)?
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…)
GROMACS: Uses & Applications
GROMACS stands for GROningen MAchine for Chemical Simulations . 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…)
Easy installation of GROMACS on Ubuntu 18.04 & 20.04
We have provided several articles on GROMACS  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…)
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 . 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…)
How to 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…)
Tutorial: MD Simulation of small organic molecules using GROMACS
Tutorial: MD simulation with mixed solvents using GROMACS
Tutorial: MD simulation output analysis of a complex using GROMACS
We have provided several tutorials on molecular dynamics (MD) simulation (please check further reading section). They include installation of simulation software, simulation of a simple protein, and a complex. In this article, we will analyze the GROMACS  output of MD simulation of a complex. (more…)
How to submit MD simulation job on a cluster server using PBS script?
Molecular dynamics (MD) simulation is one of the most widely used methods in bioinformatics. It needs high computation time and therefore, performed on workstations and servers. It requires software to upload and download files to and from the server. In this article, we have explained how to submit MD simulation jobs on cluster computers using PBS scripts. (more…)
Installing GROMOS96 on Ubuntu
GROMOS96 is a well-known software package used for biomolecular simulations . It can be used for the molecular dynamics simulation of protein, peptide, and protein-ligand complex as well. In this article, we will install GROMOS96 on Ubuntu. (more…)
MD Simulation using GROMACS: Things to remember
Molecular dynamics (MD) simulation is considered amongst the important methods in bioinformatics. Installation of MD simulation software and execution of their commands is critical. It requires several parameters to be considered before performing simulations. A single mistake may result in impractical outputs. In this article, we will discuss such important things to remember during the MD simulation and installation and execution of its software (GROMACS) [1,2]. (more…)
Video Tutorial: MD Simulation using GROMACS
Tutorial: MD Simulation of a Protein-Ligand Complex using GROMACS
Previously, we have provided a tutorial on molecular dynamics (MD) simulation of a protein using GROMACS  and its result analysis . In this article, we will perform MD simulation for a protein-ligand complex using GROMACS [3, 4]. (more…)
Installing CHARMM on Ubuntu
CHARMM (Chemistry at Harvard Molecular Mechanics) is a molecular simulation program that can be used for simulation of macromolecules, complexes, and many-particle systems . In this article, we will install the nonprofit/academic version of CHARMM on Ubuntu. (more…)