Basics

What each command does, what each configuration key means, and what a finished run looks like on disk. The tutorials are the steps; these pages are the explanations behind them, and every tutorial links here rather than repeating them.

build-top	one structure → a serialised System, the structure it matches, and a build record
Parameterising a ligand	a molecule with no residue template → a reusable parameter package
build-md	a protocol configuration → the run scripts, the .in files and run.sh
Every configuration key	the generated reference for every key build-md accepts
md-run	the Amber-like surface: flags, what each one means, and what is refused
The run layout	what a run writes, where, and which files belong to the system rather than the run
Collective variables	torsion reporting: the cv.yaml schema, cadences and outputs
Registration	turning a finished tree into a verified dataset
Ligand parameter packages	what a package is, how it is identified, and how it is reused