Installation & Updates

How to install OMMProtocol

First method: Standalone installer

If you haven’t used Anaconda or Miniconda before (a Python distribution with a cool package manager), your best bet is to simply download the installer for the latest release, which includes everything you need.

  1. Go to the OMMProtocol releases page and download the latest installer for your platform.
  2. Run the installer and follow the instructions!
    1. In Linux, open the terminal and run bash ~/Downloads/ommprotocol*.sh or whatever path the file got saved.
    2. In Windows, double click on the downloaded ommprotocol*.exe.
  3. The installer will create, by default, a new directory called ommprotocol in your $HOME. Under ommprotocol/bin``(Linux) or ``ommprotocol/Scripts (Windows) you will find the ommprotocol executable.

Second method: Conda package

OMMProtocol is also distributed as a separate conda package. If you already have Anaconda/Miniconda installed, you won’t probably want to download a separate Python distribution. In that case, skip to step 2.

  1. Download and install Miniconda, a tiny Python distribution with a cool package manager and installer. Check its webpage for more info.
For Linux:

bash Miniconda3*.sh

For Windows, download the EXE installer:
  1. Install it in the default environment…
conda install -c omnia -c insilichem ommprotocol
  1. … or use a new, separate environment (optional):
conda create -n ommprotocol -c omnia -c insilichem ommprotocol
conda activate ommprotocol
  1. If everything is OK, these sould run correctly.
ommprotocol -h
ommanalyze -h

Third method: From source

If there’s no package for your platform, install the dependencies with conda and then install ommprotocol from pip or source.

conda create -n ommprotocol -c omnia openmm ruamel_yaml parmed openmoltools mdtraj netcdf4 jinja2 pdbfixer
conda activate ommprotocol
# stable version
pip install ommprotocol
# dev version
pip install

Updating OMMProtocol

Depending on the installation method, updating OMMProtocol involves different steps.

First method: Standalone installer

Just download the installer for the new version and run it. In Linux/MacOS you will need to append the -u flag to the installer. In Windows, just follow the wizard.

Second method: Conda package

Within the activated environment, run conda update -c insilichem -c omnia ommprotocol. That’s it.

Third method: From source

Simply pass the -U flag to pip: pip install -U ommprotocol or, for development version, pip install -U