Help! How do I get started?

These instructions are intended for users from a biology, chemistry, or physics perspective who are getting started with MDTraj. It does not assume prior experience with the Python programming language or the command line.

Why Python?

MDtraj is not a standalone program. It’s a software package that provides functions for analyzing and working with molecular dynamics trajectories in python; it’s a set of building blocks.

Python is ideal because it gives you, as a scientist, the ability to mix and match, to combine tools in new ways, and to develop analyses and visualizations. You can do all of this while building on top of a wealth of high-quality open source packages for interactive scientific computing, like IPython, numpy, scipy, scikit-learn, and matplotlib.

Installing Python

Because python is free, open source, and general purpose, there are a lot of different ways to install it.

We strongly recommend that you use the Anaconda scientific python distribution, because it comes pre-installed with most of the building blocks you need for numerical and scientific computing, and with a great package manager, conda, for installing additional packages. We also like the miniconda python distribution, which is a little bit smaller and contains just python and conda.


Here’s the download link for the Anaconda scientific python distribution.

When given the option to choose which version of python, we recommend the latest, python 3.4.

On windows, we recommend using the 32-bit Anaconda installer, regardless of whether or not your operating system is 32-bit or 64-bit. On OS X and Linux, use the 64-bit python.

Installing MDTraj

After installing python, you’ll need to install mdtraj using the command line.

  • Windows: Find the Anaconda Command Prompt in the Start Menu
  • OS X: Open the Terminal application in Applications / Utilities

From the command line, type python --version. This should show the version of python you have installed. For example, the command:

$ python --version

prints out

Python 3.4.2 :: Continuum Analytics, Inc.

If everything looks good, go ahead and install mdtraj using the conda package manager.

conda install -c mdtraj

Starting MDTraj with IPython

If you’re using Windows, open the IPython Notebook from the Start Menu. For OS X or Linux, run the command ipython notebook from a command line prompt. This should load up a new notebook in your browser.

From here, you can start by trying import mdtraj, or copying a pasting commands from our examples page, and getting familiar with the environment. You’re off to the races!

Resources and Getting Help

Here are some resources that you might find useful for getting started, especially for scientists and scientific programming in Python.

Python resources:

Code Academy Introduction to Python
This web course from Code Academy is a good introduction to basic programming in Python (without a particular focus on scientific works). It covers syntax, functions, control flow, and data structures.
Scientific Python Lecture Notes
Tutorial material on the scientific Python ecosystem, a quick introduction to central tools and techniques. The different chapters each correspond to a 1 to 2 hours course with increasing level of expertise, from beginner to expert.
Lessons from the Software Carpentry
The Software Carpentry is a non-profit organization whose members teach researchers basic software skills. All their teaching material is online and freely available. They might be hosting a workshop near you too!

Getting help:

MDTraj Discussion Forums
You can ask questions in our discussion forums. It is generally quite responsive.
MDTraj Github Issue Tracker
The development activity for MDTraj takes place openly on github. This is the best way to contact the developers directly, and participate in improving MDTraj for everyone.