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MDTraj — Vecura
MDTraj
MDTraj is a Python library for reading, writing, and analyzing molecular dynamics (MD) trajectories with fast, vectorized routines for RMSD, secondary structure, hydrogen bonds, distances, dihedrals, SASA, radius of gyration and other observables.
Trajectory Settings
Syntax OK · counts shown after first run
frame
Collapse 8-letter DSSP codes into 3-class (H/E/C)
nm
RMSD Variants
Permutation-invariant RMSD
Align frames before RMSD
Baker-Hubbard H-Bonds
Adds baker_hubbard results to H-Bonding tab
Wernet-Nilsson H-Bonds
Adds wernet_nilsson results to H-Bonding tab
π-Stacking Interactions
Aromatic ring centroid distances
Custom Atom Pair Distances
Adds atom pair distances to Distances tab
Atom Pair Displacements
Vector displacement between atom pairs
Neighbor Search
Atoms within cutoff of query atoms
Radial Distribution Function
Pair correlation function
Custom Bond Angles
Angles from atom triplets
Custom Dihedral Quartets
Adds custom dihedral angles to Dihedrals tab
Shrake-Rupley SASA Advanced
Per-atom solvent accessibility
Force-Field Thermodynamics
Dynamics (PCA + Native Contacts)
Principal Component Analysis
Reduces high-dimensional motion to principal components
Native Contacts (Best–Hummer Q)
Folding order parameter
Chemical Shifts — PPM (experimental)
Requires external PPM binary
Trajectory Export
Configure input settings on the left, then click "Run"
