MD Trajectory Analyzer

Compute backbone RMSD, radius of gyration, per-residue RMSF, protein–ligand H-bond occupancy, and RMSD-based frame clusters from an OpenMM trajectory.
Estimated minimum cost: $—

Trajectory

Prefer an OpenMM MD result zip (pipeline_summary.json plus simulation/trajectory.dcd). Standalone topology PDB and DCD files are also accepted.

OpenMM result zip
or drop a file here

Analysis options

Stride and max frames control how many snapshots are analyzed. RMSD is measured against frame 0 or the topology (minimized) coordinates using the MDAnalysis selection. Ligand H-bond occupancy uses the ligand selection when those atoms exist.