Installing Gromacs on Linux, a tool for Molecular Dynamics simulation software with an overall explanation on how to install.
In bioinformatics, GROMACS is one of the most mainstream Molecular Dynamics reproduction programmings with heaps of highlights that are inherent. Introducing GROMACS Version 5.x.x+ can be a dreary and bulky procedure on Ubuntu (Linux), particularly on the off chance that you are simply beginning. For amateurs, introducing and getting GROMACS to work is all the more testing because of newness to Linux orders and GROMACS conditions. Additionally, the established guidelines for variant 5+ accessible on the GROMACS site don’t appear to work direct.
Right now, I will show you how to introduce Gromacs on Ubuntu 14.04 LTS. It is required to take a shot at any adaptation of Ubuntu. Post in remarks in the event that you face any issue.
I will likewise clarify the implications of various orders close by.
To introduce GROMACS 5+, sign in to your Ubuntu framework and open a terminal by squeezing Ctrl+Alt+T together.
You need a decent web association as we should download different conditions during the establishment procedure. To introduce Gromacs, we need the following virtual products introduced on our framework:
- A C & C++ Compiler which comes built-in with Ubuntu.
- CMake – A Linux software to make binaries
- build-essential – It is a reference for all the packages needed to compile a package.
- FFTW library: a library used by Gromacs to compute discrete Fourier transform
- DeRegressionTest Package
If you have freshly installed Ubuntu, don’t forget to update your repository information and software packages in your system. Press Ctrl+Alt+T and a terminal will open up. In the terminal, type:
sudo apt-get update
sudo apt-get upgrade
The first step in installing Gromacs is to get cmake, In the terminal, type:
sudo apt-get install cmake
If asked “After this operation, 16.5 MB of additional disk space will be used. Do you want to continue?”, Press y and then press Enter.
Easy Method Update: 2019
To make it, even more, easier to install Gromacs, We have created an installer for you. If the following installer doesn’t work, you can proceed with the normal method:
make installer executable
chmod +x gromacs-installer.sh
When download and installation finishes up, you can check the version of CMake by the following command
Next, we need to install build-essential with this command
sudo apt-get install build-essential
Before we go any further, it is good to know the path of our current working directory, in the terminal, type:
Note down the path it shows, it is very important and will be used during real Gromacs installation.
Now that we have CMake in place and we know the working directory, Its time to download Regression Tests Package. It is possible to automatically download this package during installation, but most of the time it throws me an error stating that the location of the file has changed, so let us do it the hard way to avoid any problem during installation. Copy and Paste the following commands in your terminal (Right Click to paste or Ctrl+shift+V). It basically downloads the file and saves it in your downloads folder.
We have Regression test package in our downloads folder as a compressed tar.gz archive, let us extract it with
tar xvzf regressiontests-5.1.1.tar.gz
Now we need Fourier Transform Library on our system. You can download it on fftw.org or install it from the repository with this following command
sudo apt-get install libfftw3-dev
Okay, Let us now download GROMACS 5.1.1 with this command, Alternatively, you can download the latest version from GROMACS website.
Now extract GROMACS archive
tar xvzf gromacs-5.1.1.tar.gz
Now move inside the Gromacs folder,
Create a directory called “Build” where we will keep our compiled binaries
move inside the build directory
It’s time to make Gromacs, Replace “pwdpath” with the path of a working directory that you have noted earlier in the following command:
sudo cmake .. -DGMX_BUILD_OWN_FFTW=OFF -DREGRESSIONTEST_DOWNLOAD=OFF -DCMAKE_C_COMPILER=gcc -DREGRESSIONTEST_PATH="PUT YOUR PWD PATH HERE WITHOUT QUOTES"/Downloads/regressiontests-5.1.1
Note: There is no space after any = (assignment operator) and there are no quote symbols. If you get “There is no CMakeList file in specified location”, then please check for space or incorrect path.
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. If you have forgotten it, just open another terminal and type pwd.
Now let’s first check and make the real thing.
sudo make install
Now, It may take some time depending on your configuration. After completion, execute it:
After the successful installation, you may check the version of your Gromacs with a command to make sure the installation finished as expected.
gmx pdb2gmx --version
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Installing Gromacs on Linux