Install Gromacs Molecular Dynamics Simulation software on Windows 10 by using build in Linux Subsystem WSL

GROMACS on WINDOWS

Erik Breslmayr

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Aug 25, 2020

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WSL under Windows10

• First enable WSL under Windows10 WSL
• Normally you now have WSL 1 installed, which is completely OK for Gromacs, however to use for instance xmgrace you need a GUI (graphical user interface), therefore WSL 2 is necessary.
• WSL 2 can additionally be installed under Windows10. (WSL 1 & 2)
• After you have succesfully enabled WSL you can compile a Gromacs version and run it from the command line as it would work under Linux.

Linux under Windows10

• From the “Microsoft Store” you can install any Linux distribution.
• However, I prefer Ubuntu, therefore I use Ubuntu 20
• Install and create a user account, this user doesn’t have anything to do with your Windows user account… I prefer to choose a simple name and relative simple password, because you have to type it quite often…

Compiling Gromacs

• Download any Gromacs version you would like to run from the Gromacs website. (GROMACS)
• Unpack the gromacs version, either with a Windows program such as 7zip or navigate to your “Download” folder or the folder you have downloaded Gromacs.
• Use the Ubuntu command line -> type the command

tar -xvf gromacs-20xx.x.tar.gz (change the xx to the version number of Gromacs!)

Command line

• Now you have to switch to the command line
• Navigate to the “gromacs-20xx.x” folder which appeared by using the command

cd gromacs-20xx.x

• Follow the Installation guideline from the Gromacs website (Installation)
• First we create a “build” folder with the command

mkdir build

• Than we have to install some additional programs to compile Gromacs.
• Run this commands to install necessary programs:

First update and upgrade all packages…

sudo apt-get update && sudo apt-get upgrade

Install necessary packages…

sudo apt-get install build-essential cmake libuv1-dev libssl-dev libhwloc-dev

Finally update and upgrade also the installed packages…

sudo apt-get update && sudo apt-get upgrade

• Go to the “build” folder and type:

cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON

Optional: -DCMAKE_INSTALL_PREFIX=/home/xxx/gromacs -DBUILD_SHARED_LIBS=OFF -DGMX_GPU=ON -DGMX_USE_OPENCL=ON -DGMX_MPI=ON

• Install_prefix — changes the location to install gromacs (add your home folder for instance; default is /usr/local/gromacs)
• Build_shared_libs — to turn off shared libraries (makes it more portable)
• GPU — if your system has an GPU (graphics card)
• OpenCL — for AMD GPUs OpenCl is needed for parallel computing, for Nvidia cards Cuda will automatically be used.
• MPI — Message passing interface for multicore and multiplatform calculation, only needed if you have more than one workstation (computer cluster)
• After cmake compile the program with:

make

• To check if everything went fine you can type:

make check (maybe not necessary on a local machine)

• To finally install gromacs and to make the programs executable type:

sudo make install (sudo, only if you install it in the default location)

• Now gromacs is installed on your machine, however to call it from the command-line we have to source the directory of Gromacs.
• Go to your home directory by typing cd and open the file ".bashrc"
• This file starts with an dot “.”, therefore it is hidden and only visible if you type ls -a
• For WSL 1 you can type nano .bashrc or vim .bashrc (for command-line editor)
• For WSL 2 you can type gedit .bashrc (for GUI editor)
• Add the path you have installed gromacs into this file at the beginning or the end, that does not matter.
• source /usr/local/gromacs/bin/GMXRC or source /home/xxx/gromacs/bin/GMXRC
• With this you should be fine and you can run Gromacs from the command-line with gmx