There are no official releases of MDSynthesis yet, but the master branch on GitHub gives the most current state of the package.

First install the dependencies. Since MDSynthesis uses HDF5 as the file format of choice for persistence, you will need to install the libraries either using your package manager or manually.

On Ubuntu 14.04 this will be

apt-get install libhdf5-serial-1.8.4 libhdf5-serial-dev

and on Arch Linux

pacman -S hdf5

PyTables can be particularly picky, and it often fails to obtain its own dependencies. It is best to first install PyTables’ dependencies explicitly

pip install numpy numexpr Cython

Then install PyTables and everything else

pip install tables
pip install pandas h5py MDAnalysis scandir

Then clone the repository and switch to the master branch

git clone
cd MDSynthesis
git checkout master

Installation of the packages is as simple as

python build
python install

This installs MDSynthesis in the system wide python directory; this may require administrative privileges.

It is also possible to use --prefix, --home, or --user options for to install in a different (probably your private) python directory hierarchy. python install --help should show you your options.