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.
To compile MDTraj from source, you should use pip as well:
git clone https://github.com/mdtraj/mdtraj cd mdtraj pip install -e .
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 commands
git clone https://github.com/mdtraj/mdtraj.git cd mdtraj # If using conda, make sure to have your conda environment active py.test