[[ https://www.gromacs.org/ | GROMACS Home ]]
====== Installation ======
  * Compile the source code (for gromacs-2018)
<code>
...
cmake .. -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda \
  -DGMX_MPI=on -DCMAKE_INSTALL_PREFIX=/home/usr/share/gromacs
...
</code>
  * Compile the source code (for gromacs-2016)
<code>
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
</code>

  * Set up the environment
    * Copy the stuff under /home/yxue/usr into /home/usr/share/gromacs
    * Add the following line to your ~/.cshrc
<code>
source /home/yxue/usr/bin/GMXRC.csh 
</code>

====== Setup MD simulations ======
  * See orange:/home/yxue/work/gromacs/lysozyme.demo and README file in each folder. Please also read [[http://www.mdtutorials.com/gmx/lysozyme/index.html | the online tutorial]] and [[http://cgmartini.nl/~mdcourse/pepmd/ | another tutorial]]
  * Tutorial website: http://www.mdtutorials.com/gmx/
  * How to run gromacs on GPUs: http://www.gromacs.org/Documentation/Acceleration_and_parallelization