• Compile the source code (for gromacs-2018)

...
cmake .. -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda \
  -DGMX_MPI=on -DCMAKE_INSTALL_PREFIX=/home/usr/share/gromacs
...

• Compile the source code (for gromacs-2016)

tar xfz gromacs-2016.3.tar.gz
cd gromacs-2016.3
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_MPI=on -DCMAKE_INSTALL_PREFIX=/home/yxue/usr
# NOTE: if you have GPU available, add "-DGMX_GPU=on" to the command line above
make
make check
make install

• Set up the environment
  • Copy the stuff under /home/yxue/usr into /home/usr/share/gromacs
  • Add the following line to your ~/.cshrc

source /home/yxue/usr/bin/GMXRC.csh 

• See orange:/home/yxue/work/gromacs/lysozyme.demo and README file in each folder. Please also read the online tutorial and another tutorial
• Tutorial website: http://www.mdtutorials.com/gmx/
• How to run gromacs on GPUs: http://www.gromacs.org/Documentation/Acceleration_and_parallelization