As part of the Scottish Universities Physics Alliance (SUPA), I have been giving an introductory course on molecular mechanics. The lectures slides can be found here:
CCPBioSim is a molecular modelling consortium in the UK that among other things also provides training for PhD students in molecular modelling. In 2019 I ran an introductory workshop on alchemical free energy calculations using BioSimSpace and Markov Modelling with pyEmmma.
Slides are available here:
The practical workshop material can be found on github:
If you are interested in getting started with Python, Bash, and git, checkout the Software Carpentries resource. Here is a list of Carpentries events I organised in Edinburgh:
Getting started with molecular simulations can be difficult, these best practices are a good starting point:
If you want to learn more about Markov State models the pyEmma tutorial are a good starting point: