VMD is an excellent visualization program, with powerful command-line scripting functionality. Recently, VMD’s C functions can be invoked using a set of easy to use python modules. Vmd-python is installable VMD as a Python module.

I’ve pulled some bonus features out of the source code and made it work with Python 2 or Python 3, as well as being (relatively) easy to build.

Although there is some online documentation, it is not quite complete. Here I’ve collected a full reference of all available functionality in the vmd-python module. Note that this does not include GUI features you may find helpful, such as Python callbacks or adding Tkinter menus.


  • All features of VMD from the 1.9.4 alpha release
  • DMS plugin for DESRES molecular file format
  • HOOMD plugin (with libexpat)
  • Doesn’t depend on the exact numpy version it was built agains
  • Can be built with any Python
  • Support for Python 2 or 3


I recommend using the pre-built binary packages with the Anaconda Python Distribution. Currently, there are packages available for Linux and OSX:

conda install -c conda-forge vmd-python

For other architectures, you can download the source:

python setup.py build
python setup.py install

VMD-Python has the following dependencies:

  • libnetcdf >= 4.3
  • numpy
  • libexpat