Are you using the UC Davis FARM for molecular modeling and need to figure out how to setup GROMACS? Well hello extremely small subset of the population! This is the guide for you.
Note, this is only for a basic installation. For maximum performance refer to the GROMACS guide linked above.
Getting started
We will be working off the installation instructions on the
GROMACS website
but will modify a few steps to deal with the quirks of the FARM at the time
of writing and the fact you will not have sudo privileges.
If you want to cut to the chase, you can run this script, which will run all the code in this guide in one go. Everything will be downloaded / complied in the directory you run the script in. You can use the command below to download the script, give it permission to run, and then run it.
wget http://ethanholleman.github.io/posts/code/farm_install_gromacs.sh; chmod 777 farm_install_gromacs.sh; ./farm_install_gromacs.sh
With that in mind the first thing to do is select a directory where you will
download everything, cd into it and get going.
Download and install a recent cmake version
At the time of writing, the FARM is running cmake 3.10.2 while GROMACS requires
at least 3.13.0 to build. I will be downloading 3.19.2 as it is the most
recent at the time of writing. If you are downloading a different version
you will have to modify some of the commands to reflect that (this will be
true for all downloaded programs).
Download and run the install with the commands below
wget https://github.com/Kitware/CMake/releases/download/v3.19.2/cmake-3.19.2-Linux-x86_64.sh
chmod 777 cmake-3.19.2-Linux-x86_64.sh
echo "Running cmake installer"
./cmake-3.19.2-Linux-x86_64.sh
Download and compile GROMACS
Download your preferred version of GROMACS from the docs,
I will be using 2021-rc1 for this guide.
wget http://ftp.gromacs.org/pub/gromacs/gromacs-2021-rc1.tar.gz
tar xfz gromacs-2021-rc1.tar.gz
Now enter into the newly downloaded GROMACS directory and create a build directory.
cd gromacs-2021-rc1
mkdir build
cd build
From the build directory run the newly downloaded cmake version by determinging
the path to the cmake exe. It will be located in folder produced by the cmake
installer. For me, the full path was
/home/ethollem/software/cmake-3.19.2-Linux-x86_64/cmake-3.19.2-Linux-x86_64/bin/cmake.
Then run cmake with your version subsituted into [cmake] below.
[cmake] .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
Then make the program (this could take a while).
make
make check
The GROMACS guide recommends the following command
sudo make install
but since we do not have sudo privileges to run the program we can add the
exe to out PATH variable. From the
build directory the GROMACS exe path will be [Your absolute path to build dir]/bin/gmx.
For me this looks like home/ethollem/software/gromacs-2021-rc1/build/bin/gmx.
Open / create ~/.bashrc using your preferred text editor and add the line
export PATH="$HOME/software/gromacs-2021-rc1/build/bin/gmx:$PATH"
Then log off and log back in again. Test everything is working correctly by running
gmx --help
You should be greeted wih the GROMACS help page. If you are you are now good to go.