New to Python

These instructions are intended for users from a biology, chemistry, or physics perspective who are getting started with MDTraj and may be unfamiliar with Python or programming.

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 the ability to mix and match or combine tools in new ways. You can truly 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

There are multiple ways to install Python. We strongly recommend that you use the Anaconda distribution, which is aimed towards scientists. 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.


Download Anaconda scientific python. Pick Python 3.5

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 3.5.1 :: Continuum Analytics, Inc.

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

conda install -c conda-forge mdtraj

The conda-forge “channel” provides a variety of packages supported by the Python community.

Starting MDTraj with IPython/Jupyter

If you’re using Windows, open the Jupyter Notebook from the Start Menu. For OS X or Linux, run the command jupyter 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.