This is an open educational resource originally developed for postgraduate taught masters chemistry students at the University of Edinburgh to introduce the practical aspects of molecular dynamics simulations.
This course is designed for students with no prior experience in programming or computational chemistry. It is delivered over a month as a series of four 3-hour workshops in a computer-lab setting, with the final session dedicated to individual projects.
The course aims to equip students with practical skills necessary to perform meaningful molecular dynamics simulations, including:
- Using basic command-line interfaces;
- Navigating and utilising high-performance computing resources;
- Preparing, running, and troubleshooting molecular dynamics simulations using GROMACS software;
- Recognising the limitations of computational chemistry methods available;
- Applying these skills independently to real research systems.
In this repository, and with the associated manuscript, we share the materials with the hope that their future reuse and adaptation will benefit chemistry education across the globe.
- Lectures - each session begins with the introductory lecture, and all the slides are shared within.
- Notes - HTML materials for self-guided work during each session. Start by opening
Overview.htmlin your browser. Dyslexia-friendly settings are also available. - Practicals - all the files necessary to complete each session.
Please note that we are not sharing the materials for Session 4, as those are used for a summative assessment. Nevertheless, we share an example report and the templates.
- Sarah V Stewart - testing material for 2023/24, adaptation of the original materials for 2024/25, development of MedBio materials in Sessions 3 and 4, overseeing the module delivery in 2024/25, delivery of materials in Session 1, demonstrating in 2023/24 and 2024/25.
- Hannah Pollak - development of the original course materials in 2023/24, integration of Dyslexia-friendly settings, creation of virtual machine template, set up of virtual machines in 2023/24, benchmarking of computational resources, set up of storage space, overseeing the module delivery in 2023/24, demonstrating in 2023/24.
- Timothy J. Spankie - development of the MedBio materials in Sessions 3 and 4, delivery of MedBio materials in Session 3, demonstrating in 2024/25.
- Audrey Ngambia - delivery of materials in Session 2, testing the materials, demonstrating in 2023/24 and 2024/25.
- Angela Chitzanidi - set up of virtual machines, ensuring access to HPC facilities for all students.
- Valentina Erastova - module lead, development of original materials, full oversight of the development and delivery of the module, delivery of teaching materials in all sessions.
- Software Carpentry lessons
- Carpentry Community lessions
- GROMACS tutorials
- CCPBioSim workshop
- ClayCode workshop
- VMD
- GROMACS version
gromacs/2024.4was used for simulations throughout this course. - VMD version
1.9.4was used for rendering of images. - Xmgrace version
5.1.25was used for plotting.
The easiest way is by cloning the material and adapting it to your needs. This can be just using some partial material or expanding on the existing material. The best way to do this is by either cloning the repo and building up on it, or using the current repository as a template repository for your own or your organisations GitHub account.
If you are interested in using the material outside of the University of Edinburgh, or already have access to a Unix machine/virtual machine, the instructions will need adapted. At the end of each session's introduction page there is a link and QR code to a Wooclap feedback form. If you wish to gather your own feedback, you will need to regenerate the form and update the links and codes.
If you have access to a Unix machine (e.g. Linux desktop, MacOS), you will not need a virtual machine and so can ignore/remove material from lecture 1. If you are using a different virtual machine platform, adapt these sections accordingly. The material was developed and tested on the dependencies listed above and on the hardware listed in the paper.
We strongly recommend using an HPC to run the simulations. If you don't have access to one, the length of the simulations will need to be reduced according to the available hardware. For example, the production simulation in Session 2 ran at 355 ns/day on the Eddie HPC and will instead run at 5 ns/day on an Apple M2 MacBook Pro. The instructions in session 1 part 3, session 2 parts 2 & 3, session 3 parts 2 & 3, and session 4 task list and any corresponding .mdp files will need adapted.
If you have access to a different HPC, you would need to adjust the access details in session 1 part 3, session 2 parts 2 & 3, session 3 parts 2 & 3, and session 4 task list, and generate new .sh files for simulation submission to the scheduler. Note that Eddie HPC uses the Altair Grid Engine Scheduler and the simulations are run on GPUs.
Contributions to the learning resource are welcome. Contributions can be made through creating an issue or a pull request.
- To create an issue, contributors are encouraged to follow the GitHub quickstart guide on creating an issue.
- Make sure to include the following into your issue:
- What version of the different packages are you running
- Are you using it as a student or instructor?
- Is the issue reporting a bug, an enhancement, or a feature request
- To create a pull request, contributors are encouraged to follow the GitHub quickstart guide on creating a fork and submitting a pull request.
If you just want to tell us how you have been using the resource just send us an email or raise an issue pointing to your work.
If using this material, please acknowledge the developers and cite the associated publication:
- JOSE REFERENCE WHEN AVAILABLE
These materials are made freely available, and are licensed under a CC-BY 4.0 license.