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README.md

Protein MD Setup tutorial using BioExcel Building Blocks (biobb)

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).


Settings

Biobb modules used

  • biobb_io: Tools to fetch biomolecular data from public databases.
  • biobb_model: Tools to model macromolecular structures.
  • biobb_md: Tools to setup and run Molecular Dynamics simulations.
  • biobb_analysis: Tools to analyse Molecular Dynamics trajectories.

Auxiliar libraries used

  • nb_conda_kernels: Enables a Jupyter Notebook or JupyterLab application in one conda environment to access kernels for Python, R, and other languages found in other environments.
  • nglview: Jupyter/IPython widget to interactively view molecular structures and trajectories in notebooks.
  • ipywidgets: Interactive HTML widgets for Jupyter notebooks and the IPython kernel.
  • plotly: Python interactive graphing library integrated in Jupyter notebooks.
  • simpletraj: Lightweight coordinate-only trajectory reader based on code from GROMACS, MDAnalysis and VMD.

Conda Installation and Launch

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_MDsetup_tutorial
jupyter-nbextension enable --py --user widgetsnbextension
jupyter-nbextension enable --py --user nglview
jupyter-notebook biobb_wf_md_setup/notebooks/biobb_MDsetup_tutorial.ipynb

Tutorial

Click here to view tutorial in Read the Docs

Click here to execute tutorial in Binder


Version

2020.4 Release

Copyright & Licensing

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).

Licensed under the Apache License 2.0, see the file LICENSE for details.

About

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).

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