mdtraj-trajectory-analysis
From the author
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.
Install
npx skills add jaechang-hits/SciAgent-Skills --skill mdtraj-trajectory-analysis -a claude-code
Installs to .claude/skills/mdtraj-trajectory-analysis/ · Each command fetches the skill straight from GitHub with the open skills CLI.
No download: this skill’s licence (LGPL-2.1) does not let us redistribute its files. The install commands fetch them from GitHub instead.
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