MDTraj (Claude Skill)

Mdtraj molecular dynamics trajectory analysis (Python).

   
Type Claude Skill
Supplier jaechang-hits (community OSS, CC BY 4.0)
Availability GA — part of the BixBench-evaluated SciAgent-Skills collection
Pricing Free / OSS (LGPL-2.1)
Capabilities Read/Write — Claude runs the skill’s Python locally (Bash), not as an MCP tool

How to install

SciAgent-Skills is not an npm package — skills are plain markdown read directly by the agent (no npx/npm).

  • Claude Code — clone and load as a plugin: 
    git clone https://github.com/jaechang-hits/SciAgent-Skills

    Then inside Claude Code run /plugin install sciagent-skills (verify it appears under /plugin → Installed). Clone into your project directory so Claude Code picks the skills up via CLAUDE.md.

  • Manual / other agents — point the agent at the skill file directly: 
    cp -r SciAgent-Skills/skills/structural-biology-drug-discovery/mdtraj-trajectory-analysis ~/.claude/skills/

    The skill declares its own Python dependencies in its SKILL.md; install them when prompted on first use.

What it does

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.

Primary use cases: Mdtraj molecular dynamics trajectory analysis (Python).

Notes

Distributed as a SKILL.md (plus code examples) in the SciAgent-Skills collection — Claude executes it locally via Bash/Python rather than as an MCP server. Upstream license: LGPL-2.1. The skill directory upstream is skills/structural-biology-drug-discovery/mdtraj-trajectory-analysis.

Sources

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