Tutorial describing detailed workflow for creating and analyzing trajectories produced by the most popular simulation packages using vanila python and open source Python libraries..
What you will learn:
- what are most popular tools to do MD
- popular data formats and python tools to work with them
- how to prepare robust and easy to set up work environment
- how to build MD system
- how to run MD simulations using most popuar packages
- how to dock small ligands
- how to scale up/out your simulations
- how to load a structure or a MD trajectory (popular formats)
- how to select parts of your system
- how to work with atoms, residues and molecules
- how to deal with large data-sets (bigger than RAM)
- how to analyze MD trajectories
- how to write out or convert trajectories
- how to use various algorithms in analysis (clusterization, structure, ML)
- how to build interactive visualizations