(Remarks 2026: the SimplifyEval repository linked in 2022-training that contains double-click docking scripts and question-driven self-study materials is currently set to private for maintenance.)
Collection of educational materials and project files prepared for my teaching duties since I have started learning to do molecular modelling, in particular molecular dynamics (MD) simulation.
Handouts and tutorials in this work are licensed under a
CC-BY-NC-SA 4.0 License.
A 64-bit Windows-only "portable" package of CPU Gromacs binary (Version 2019.6) bundled with several analysis tools can be found in "Releases" for easy installation and usage. However, I DO NOT own the copyright of Gromacs, QTGrace and Jmol; NOR do I own copyright of the documents included in the "doc" directory in the package. Please refer to the corresponding license file for the information.
For a more updated or GPU-accelerated version of GROMACS binary on Windows, please refer to other sources, e.g. from these repositories or compile it yourself for optimized performance.
A detailed description on MDportable bundle can be found in "README_MDportable.txt" which is also included in the zip archive in Release.
Targeting students who may panic when they need to use command-line. Part of the materials aimed to provide these students with a brief experience of what is molecular modelling and MD. Such simplified methods may not ideal for learning the technique in practice. Hence the name of "MD-zero" of the repository, it's not yet "MD-101" in terms of teaching.
- Also include materials of other molecular modelling techniques which is not necessarily MD.
- I aquired my (minimal) programming skill via self-teaching, i.e. pseudo-code + Googling + (minimal) reference book. The code may not be optimized or following best-practices. Please feel free to comment on how to improve the code!
- For details and related references of different projects, please refer to the README file in the corresponding directory.
Here is a list of software have the potential to be utilized in future educational projects. They are lacking some important features which forced me to stay with other programs for now, but I look forward to their future development.
- Foldit and FolditStandalone
- Advantage: Foldit is a video game of protein modelling, protein design, and small-molecule design that use ROSETTA as the backend. It is a molecular modelling program but not a MD software. It has comprehensive biochemistry tutorial and provides game-like hands-on experience on molecular modelling.
- Disadvantage: Foldit/FolditStandalone only has limited support for non-protein. Setting up custom puzzle is also tricky and may require additional tools.
- UCSF ChimeraX
- Advantage: Allows interactive MD simulation within the GUI.
- Disadvantage: Limited forcefield parameters, currently only for protein with standard amino acids and an addition set of small-molecules. Requires a recent version of OpenGL and not available on CentOS7 server.
- QwikMD GUI of NAMD in VMD
- Advantage: As the native GUI of NAMD, provides a GUI for MD setup, real-time monitoring and optionally interactive MD.
- Disadvantage: GUI not very attractive for novice users. It can be tricky to setup the interface, and the real-time simulation can be slow/freezing during the run (depends on hardware).
- Dynamics plugin for PyMOL
- Advantage: This is a PyMOL plugin that provides a GUI to configure and analyse GROMACS simulations within PyMOL.
- Disadvantage: Limited options for simulation, especially in the choice of forcefield.
- Galaxy Platform
- Advantage: A web server for life-science research including molecular modelling. Provides an exhaustive collection of tools and workflow on cloud with user-friendly GUI, no installation is needed.
- Disadvantage: It is a server, experimental collaborators may have concerns about submitting unpublished data to a server hosted by other institutions. Limited options implemented in the GUI.