MD Setup for MAPK11 using BioBB

Based on the workflow from BioBB which in turn is based NOT on an official GROMACS tutorial, but justin lemkul's

This is not a tutorial but a public workflow for testing its utility on MAPK11.

Settings

Biobb modules used

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/esguerra/mapk11
cd mapk11
conda env create -f conda_env/environment.yml python=3.7
conda activate mapk11
jupyter-nbextension enable --py --user widgetsnbextension
jupyter-nbextension enable --py --user nglview
jupyter-notebook mapk11/notebooks/mapk11_wf.ipynb

Version

2021.1 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.