Installation under windows is possible through Windows Subsystem for Linux (WSL).

If your Windows version does not support WSL, you may attempt an installation in Cygwin, but this method is no longer supported and may yield many unexpected problems.

To enable WSL on your windows installation and install a distribution, please follow the quickstart quide within WSL documentation.

Generic Python installation

With WSL enabled and your distribution of choice installed, launch WSL within PowerShell:


Then continue to install AQUA-DUCT normally as in any Linux distribution.

The easiest way to install AQUA-DUCT is to install Python 3 and use following command:

pip3 install aquaduct

While normally a pip installation should install all dependencies automatically, due to an issue with some pip packages (in this case it’s MDAnalysis[amber]) installing AQUA-DUCT may yield an error:
RuntimeError: Python version >= 3.5 required.
In which case installing numpy and scipy packages separately before installing AQUA-DUCT will solve this issue.

Please keep in mind that AQUA-DUCT and all its dependencies need to be installed for the same user

Installation of PyMOL

Under most modern GNU/Linux distributions PyMOL is available as a package in repositories. For example if you are under Ubuntu/Debian you can install it by following command:

sudo apt-get install pymol

Under Windows there are several ways to install PyMOL, for more details see PyMOL web site.

Cygwin installation (discontinued)

Installation on Windows natively may also be possible. The limiting factor is MDAnalysis which is not officially available under Windows yet. You can, however, install Cygwin and perform Aqua-Duct installation in Cygwin.

1.  Cygwin installation. During the setup select following packages:

  • python (2.7)
  • python-devel (2.7)
  • python-cython
  • libnetcdf-devel
  • libhdf5-devel
  • liblapack-devel
  • libopenblas
  • python-numpy
  • python-six

2. C, C++ and Fortran compilers installation. You can simply install gcc-g++ and gcc-fortran packages as a first choice, select following packages:

  • gcc-g++
  • gcc-fortran

3. After Cygwin installation with all required libraries, perform following steps:

# install pip
easy_install-2.7 pip

First, try to install SciPy:

# install SciPy
pip install scipy

If you encounter any problems related to missing xlocale.h header file try the following workaround:

# prepare fake xlocale.h
ln -s /usr/include/locale.h xlocale.h
export CFLAGS="I"$( pwd )

# install SciPy
pip install scipy


The above procedure for SciPy installation might not be optimal. For more information please got to SciPy web page.

4. Now, install scikit-learn and then Aqua-Duct:

# install scikit-learn
pip install scikit-learn

# finally, install aquaduct
pip install aquaduct