Up to date version is now in the OpenMM organisation: https://github.com/openmm/openmm_workshop_july2023

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OpenMM workshop

This repository contains the materials for the OpenMM workshop delivered on 12th July 2023 after the CCPBioSim conference.

The workshop consists of an introduction presentation, setup information, and a series of jupyter notebooks.

Introduction

This is a powerpoint presentation. The slides can be found in ./slides

Setup

There are two ways to run the workshop notebooks:

• In a web browser with Google Colab.
• Running locally on your own machine in a Conda environment.

The instructions for either can be found in ./setup.

Note that we have designed the exercises to not be computationally expensive so they can be run on any hardware.

Training materials

The material is in the form of jupyter notebooks. It is split up into three sections.

Section 1 - Introduction to OpenMM

• Protein in water. Aimed at people new to OpenMM. This covers loading in a PDB file, setting up a simulation, running the simulation, basic analysis, and advice for running on HPC resources.
• Protein-ligand complex. Aimed at beginners. Covers parameterising a small molecule, combining topologies, and using other tools to create OpenMM compatible input.

Section 2 - Custom forces

• Custom forces and Umbrella sampling. Aimed at people looking to use the custom forces functionality of OpenMM (Can be done after section 1 material if you are a beginner). Covers using custom forces with a case-study of umbrella sampling.

Section 3 - Machine Learning Potentials

• Machine Leaning Potentials. Aimed at people using Machine Learning Potentials. Covers the OpenMM Machine Learning software stack with examples of using ANI and MACE.

Extras

• Guide on building OpenMM from source.
• Using the different platforms.