Python tutorials for OpenMM

This guide is a set of Jupyter notebooks intended to help researchers already familiar with molecular dynamics simulation learn how to use OpenMM in their research and software projects.

Getting started

We recommend you use miniconda and the conda package manager. If you don't already have miniconda installed, you can easily install it from the terminal:

# For Mac OS X, substitute `MacOSX` for `Linux` below
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash -b ./Miniconda3-latest-Linux-x86_64.sh -p $HOME/miniconda
export PATH=$HOME/miniconda/bin:$PATH

Install the dependencies with conda:

conda install --yes -c omnia -c conda-forge jupyter notebook openmm mdtraj nglview

Tutorial modules

• 01 - Creating and importing molecular systems in OpenMM
• 02 - Integrators and sampling

More resources

Be sure to check out the OpenMM Documentation site http://docs.openmm.org, which contains an excellent User Guide, Python API reference, and more tutorials.