mdanalysis-trajectory

To compute RMSD and RMSF from a molecular dynamics trajectory, you load your topology and trajectory files into an MDAnalysis universe and apply alignment-based distance metrics to extract structural deviation and per-residue flexibility over time.

Yes, you can track hydrogen bonds and generate contact maps in MDAnalysis by applying hydrogen bond criteria and optional cutoff aggregation to produce residue-resolved interaction summaries and distance matrices for your trajectory.

Yes, this trajectory analysis approach works with GROMACS, AMBER, NAMD, and LAMMPS files by loading their topology and trajectory inputs into the MDAnalysis universe to process time-resolved coordinates.

You measure protein-ligand distances by calculating centroid or pocket-distance time series from your trajectory frames, producing quantitative outputs that show whether the ligand remains in the binding pocket throughout the simulation.

The best way to export RMSD and hydrogen bond data for reporting is to save the computed metrics into pandas DataFrames and CSV files, which provides structured data suitable for downstream statistics and publication-ready matplotlib plots.