Based on the official GROMACS tutorial.
This tutorial aims to illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Lysozyme protein (PDB code 1AKI).
- biobb_io: Tools to fetch biomolecular data from public databases.
- biobb_model: Tools to model macromolecular structures.
- biobb_gromacs: Tools to setup and run Molecular Dynamics simulations.
- biobb_analysis: Tools to analyse Molecular Dynamics trajectories.
- jupyter: Free software, open standards, and web services for interactive computing across all programming languages.
- nglview: Jupyter/IPython widget to interactively view molecular structures and trajectories in notebooks.
- plotly: Python interactive graphing library integrated in Jupyter notebooks.
- simpletraj: Lightweight coordinate-only trajectory reader based on code from GROMACS, MDAnalysis and VMD.
git clone https://github.com/bioexcel/biobb_wf_md_setup.git
cd biobb_wf_md_setup
conda env create -f conda_env/environment.yml
conda activate biobb_GMX_MDsetup_tutorial
jupyter-notebook biobb_wf_md_setup/notebooks/biobb_MDsetup_tutorial.ipynb
Click here to view tutorial in Read the Docs
Click here to execute tutorial in Binder
2023.3 Release
This software has been developed in the MMB group at the BSC & IRB for the European BioExcel, funded by the European Commission (EU H2020 823830, EU H2020 675728).
- (c) 2015-2023 Barcelona Supercomputing Center
- (c) 2015-2023 Institute for Research in Biomedicine
Licensed under the Apache License 2.0, see the file LICENSE for details.