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Running on your own machine with a Conda environment

Installing Conda

Please refer to the Conda documentation and follow the steps for installing Miniconda for your operating system.

Creating and activating a Conda environment

Create a new empty conda environment:

conda create -n openmm

Activate the new environment:

conda activate openmm

OpenMM can now be installed in this environment from the conda-forge repository using the following command:

conda install -c conda-forge openmm

Finally, test the OpenMM installation by running:

python -m openmm.testInstallation

If everything is working, the output should look similar to below (note that if you do not have a GPU, you will not see the OpenCL or CUDA platforms):

Output 
OpenMM Version: 8.1.2
Git Revision: 440a9c7ae5df23ea1ab93798a422b6d9fd3ada99

There are 4 Platforms available:

1 Reference - Successfully computed forces
2 CPU - Successfully computed forces
3 CUDA - Successfully computed forces
4 OpenCL - Successfully computed forces

Median difference in forces between platforms:

Reference vs. CPU: 6.288e-06
Reference vs. CUDA: 6.74286e-06
CPU vs. CUDA: 7.34247e-07
Reference vs. OpenCL: 6.73115e-06
CPU vs. OpenCL: 7.46613e-07
CUDA vs. OpenCL: 1.68633e-07

All differences are within tolerance.

Jupyter

To run the Jupyter notebooks in this workshop, you need to install Jupyter in your conda environment:

conda install -c conda-forge jupyter

Then, you can open the notebook in your web browser using the following command:

jupyter notebook <notebook>.ipynb

Alternatively, you can open the notebook in VS Code and install the Jupyter extension.

Mamba vs Conda

Note that our example notebooks all use mamba install ... commands.

mamba is a drop in replacement for conda that is significantly faster at solving environments and installing the packages. We recommend using mamba for improved performance. Note, however, that all mamba install commands can be replaced with conda install and should work the same way.

Once you have a working conda installation, you can install mamba with the following line:

conda install mamba -n base -c conda-forge

Getting the notebooks

You can get the notebooks and materials for this workshop by git cloning this repo:

git clone https://github.com/openmm/openmm_workshops.git