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 nose, which you can pick up via pip if you don’t already have it.

pip install nose

Then, to run the tests, execute the command

nosetests mdtraj -v

Compiling From Source

To compile MDTraj from source, you’ll need cython in addition to the normal, runtime dependencies. Check devtools/conda-recipe/meta.yaml for a complete list of build and run dependencies.