MD is a great entry point for anyone interested in scientific computing. A naive simulation is super easy to implement but you quickly learn hard lessons regarding performance scaling. I wrote an MD engine as a demo project for learning the basics of CUDA C.
For anyone with further interest in MD, two of the popular engines, Amber and Gromacs have excellent documentation for learning (1, 2). MDAnalysis is a popular analysis package. Their docs give a great rundown of what type of information you can glean from MD (3). If you’re strictly interested in eye candy, there’s a a fabulous blender plugin for visualizing MD simulations and protein structures (4). I also wrote a little Python program for setting up simulation systems you can do some fun stuff with it (5).
For anyone with further interest in MD, two of the popular engines, Amber and Gromacs have excellent documentation for learning (1, 2). MDAnalysis is a popular analysis package. Their docs give a great rundown of what type of information you can glean from MD (3). If you’re strictly interested in eye candy, there’s a a fabulous blender plugin for visualizing MD simulations and protein structures (4). I also wrote a little Python program for setting up simulation systems you can do some fun stuff with it (5).
(1) https://ambermd.org/Manuals.php
(2) https://manual.gromacs.org/current/index.html
(3) https://www.mdanalysis.org/pages/documentation/
(4) https://bradyajohnston.github.io/MolecularNodes/
(5) https://github.com/AppleIntusion/MMAEVe