We recommend that you install mdtraj with conda.

$ conda install -c conda-forge mdtraj

You can install also mdtraj with pip, if you prefer.

$ pip install mdtraj

Conda is a cross-platform package manager built especially for scientific python. It will install mdtraj along with all dependencies from a pre-compiled binary. If you don’t have Python or the conda package manager, we recommend starting with the Anaconda Scientific Python distribution, which comes pre-packaged with many of the core scientific python packages that MDTraj uses (see below), or with the Miniconda Python distribution, which is a bare-bones Python installation.

MDTraj supports Python 2.7 or Python 3.4+ (recommended) on Mac, Linux, and Windows.

Testing Your Installation

Running the tests is a great way to verify that everything is working. The test suite uses pytest, which you can pick up via pip if you don’t already have it.

pip install pytest

Then, to run the tests, execute the command

pytest mdtraj -v

Compiling From Source

To compile MDTraj from source, you should use pip as well:

git clone
cd mdtraj
pip install -e .