MDAnalysis

A set of tutorials that demonstrate how NanoVer can be interfaced with MDAnalysis to visualise static structures and trajectories in VR, and analyse the results of trajectories recorded using NanoVer.

The Jupyter notebook tutorials that showcase these features can be found in the examples folder of the GitHub repository. It contains:

• mdanalysis_lsd: A notebook that demonstrates how to import a pdb into MDAnalysis and visualise this structure in VR, including changing the visualisation of different parts of the system, e.g. protein/ligands/lipids, using MDAnalysis selections.

• mdanalysis_trajectory: A notebook that demonstrates how to import a trajectory into MDAnalysis from the topology (pdb) and trajectory (dcd) files and show this in VR. Learn how to hook up python commands such as play/pause/reset to the corresponding buttons on the handheld menu in the VR application.

• mdanalysis_nanover_recording: A notebook that details how to use MDAnalysis to extract data from an iMD simulation recorded with NanoVer, and highlights some of the benefits of recording trajectories using the in-built recording functionality of NanoVer.