Tutorial¶

A hands-on notebook that runs a complete protein–ligand molecular dynamics simulation with the workflows in this repository — in just three commands. The system is the T4 lysozyme L99A/M102Q mutant (PDB 3HTB) in complex with 2-propylphenol (ligand JZ4), the classic GROMACS protein–ligand example.

Step	Command	What it does
1	`protein_preparation`	Clean, fix and protonate the protein
2	`ligand_parameterization`	Build a GROMACS topology + coordinates for JZ4
3	`md_gromacs`	Setup → energy minimization → NVT/NPT equilibration → production MD → analysis

The notebook then visualizes the trajectory and plots the analyses (RMSD, radius of gyration, RMSF, ligand RMSD) produced by the MD workflow.

The tutorial can be run either on Google Colab (no local install) or on a local Jupyter.

Run on Google Colab¶

Click the badge above and run the first setup cell. It builds the biobb_md_tutorial conda environment from notebooks/colab_environment.yml (GROMACS, AmberTools, acpype, the BioBB packages, this repo’s workflows, and the visualization libraries) — nothing to install on your machine. The conda solve is the slow part; run it once and wait.

Run locally¶

Create the environment from notebooks/local_environment.yml, then launch Jupyter from it:

git clone https://github.com/NBDsoftware/biobb_md_workflows.git
cd biobb_md_workflows
conda env create -f notebooks/local_environment.yml
conda activate biobb_md_tutorial
jupyter notebook notebooks/notebook_tutorial.ipynb

The notebook lives at notebooks/notebook_tutorial.ipynb in the repository.