BioBB MD Workflows

Ready-to-use command-line pipelines for molecular dynamics (MD) simulations with GROMACS, built on top of BioExcel Building Blocks (BioBB). Developed for the European BioExcel project, funded by the European Commission (EU Horizon Europe 101093290).

This repository covers protein preparation, ligand parameterization, MD with GROMACS, and trajectory post-processing. Related pipelines live in separate repositories: virtual screening in biobb_vs_workflows.

BioExcel BioExcel

New here? Start with the Tutorial — a guided, end-to-end protein–ligand MD run you can do on Google Colab (no install) or on a local Jupyter.

Workflows

Command

Purpose

protein_preparation

Clean, protonate, and fix a raw PDB structure for MD.

ligand_parameterization

Generate GROMACS/AMBER topology + coordinates for ligands and cofactors.

md_gromacs

Full GROMACS MD: setup → equilibration → production → post-processing.

traj_postprocessing

Strip solvent, center, image, and fit an existing trajectory.

Licensing

Offered under a dual-license model: free for academic and non-commercial use under CC BY-NC-SA 4.0; a separate commercial license is required for for-profit use (contact it@nostrumbiodiscovery.com). See the LICENSE file in the repository.