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 (biobb) and connecting remotely to a super computer in order to run some jobs. 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_md: Tools to setup and run Molecular Dynamics simulations.
- biobb_analysis: Tools to analyse Molecular Dynamics trajectories.
- biobb_remote: Biobb_remote is a package to allow biobb's to be executed on remote sites through sshs.
- 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.
git clone https://github.com/bioexcel/biobb_wf_md_setup_remote.git
cd biobb_wf_md_setup_remote
conda env create -f conda_env/environment.yml
conda activate biobb_MDsetupRemote_tutorial
jupyter-nbextension enable --py --user widgetsnbextension
jupyter-nbextension enable --py --user nglview
jupyter-notebook biobb_wf_md_setup/notebooks/biobb_MDsetupRemote_tutorial.ipynbClick here to view tutorial in Read the Docs
Click here to execute tutorial in Binder
2021.2 Release
This software has been developed in the MMB group at the BSC & IRB for the European BioExcel, funded by the European Commission (EU Horizon Europe 101093290, EU H2020 823830, EU H2020 675728).
- (c) 2015-2021 Barcelona Supercomputing Center
- (c) 2015-2021 Institute for Research in Biomedicine
Licensed under the Apache License 2.0, see the file LICENSE for details.
