Individual skill

mdtraj-trajectory-analysis

mdtraj molecular dynamics trajectory analysis (Python). Reads DCD/XTC/TRR/NetCDF/H5/PDB topologies and trajectories; computes RMSD vs time, radius of gyration, per-residue RMSF, residue-residue contact frequency maps, phi/psi torsions for Ramachandran plots (general + Gly/Pro), and 8-state DSSP secondary structure. Modules: trajectory I/O, geometry (distances/angles/dihedrals), structural analysis (RMSD/Rg/RMSF/SASA), contacts, hydrogen bonds, secondary structure (DSSP), NMR observables. For broader atom-selection grammar use mdanalysis-trajectory; for running MD simulations use OpenMM/GROMACS.

skills/structural-biology-drug-discovery/mdtraj-trajectory-analysis/SKILL.md

Source commit 55c1bd3e863d11bf5a853d24bcdda10c88e6eddf

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Observed behavior

Network or broad shell

Last checked

Nov 5, 2026

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