GROMACS compilation

To compile custom GROMACS with PLUMED and ProDy under Ubuntu do as follow:

Add dynamics repository and install PyMOL, PLUMED and ProDy:

sudo add-apt-repository ppa:tomaszm/dynamics

sudo apt-get install pymol plumed python-prody

Install basic building tools:

sudo apt-get install build-essential cmake git

Install GROMACS dependencies:

sudo apt-get build-dep gromacs

Download latest GROMACS

git clone git://git.gromacs.org/gromacs.git

Apply PLUMED patches:

cd gromacs

plumed patch -p --shared

Follow patch instruction and after it, configure and compile GROMACS:

mkdir build_dir

cd build_dir

cmake -DCMAKE_INSTALL_PREFIX=../install -DGMX_OPENMP=ON ..

make install

Set environment variables:

export LD_LIBRARY_PATH=/home/user-name/Dokumenty/gromacs-5.?.?/install/lib

export PATH=/home/user-name/Dokumenty/gromacs-5.?.?/install/bin:$PATH

and start PyMOL:

pymol