Tutorial Overview¶

This section is the central catalog for the project tutorials. Each page is written as a practical guide with clear scope, required inputs, execution outline, and expected outputs.

Core Tutorials¶

Tutorial	Focus
Enzeptional (GT4SD)	Enzyme prediction and optimization using reaction-aware feasibility and activity estimates.
Hydrated Docking	Molecular docking with explicit water molecules in the binding site.
Molecular Dynamics with AMBER	Classical MD for protein-ligand systems, including preparation, equilibration, production, and analysis.
Molecular Dynamics with GROMACS	GROMACS-based MD workflows with trajectory processing and free-energy analysis.
SLURM for Molecular Simulation Workflows	HPC job submission and monitoring for AMBER, GROMACS, and MMPBSA jobs.
DFTB3 QM/MM with AMBER	DFTB3-based QM/MM simulation and mechanism-distance analysis for invertase/sucrose.
QM/MM with AMBER and QUICK	Hybrid quantum/classical simulation with AMBER and QUICK.
QM/MM with GROMACS and CP2K	QM/MM workflows with GROMACS coupled to CP2K.

Quick References¶

Guide	Focus
Docker Commands	Images, containers, volumes, cleanup, backup, and restoration.
Git Commands	Configuration, branches, commits, inspection, and recovery.
Simulation Scripts	AMBER replica execution and cpptraj post-processing workflows.

Documentation Standard¶

Each tutorial should define:

• the scientific or computational goal
• required software and input files
• a reproducible command sequence
• expected output files
• validation checks
• adaptation notes for other systems or clusters