mdanalysis-trajectory SKILL.md skillA
mdanalysis-trajectory from jaechang-hits/sciagent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add jaechang-hits/sciagent-skills/mdanalysis-trajectory@git:20260428.81ea2d2Pins git:20260428.81ea2d2 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- jaechang-hits/sciagent-skills
- Path
skills/structural-biology-drug-discovery/mdanalysis-trajectory/SKILL.md- Versions recorded
- 2
- Latest version
- git:20260428.81ea2d2, committed Apr 28, 2026
- First version recorded
- Feb 18, 2026
- Size
- 14,272 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
Analyze MD trajectories from GROMACS, AMBER, NAMD, CHARMM, LAMMPS. Reads topology/trajectory into Universe objects; supports RMSD, RMSF, radius of gyration, contact maps, H-bonds, PCA, and custom distance/angle calculations. Use for post-simulation structural analysis; use OpenMM/GROMACS for running simulations.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# MDAnalysis — Molecular Dynamics Trajectory Analysis ## Overview MDAnalysis provides a uniform Python interface for reading and analyzing molecular dynamics trajectories regardless of MD engine (GROMACS, AMBER, NAMD, CHARMM, LAMMPS, OpenMM). It represents molecular systems as `Universe` objects containing an `AtomGroup` with positions, velocities, forces, and topology data. Trajectories are iterated frame-by-frame or analyzed in bulk using analysis modules for RMSD, RMSF, radius of gyration, hydrogen bonds, solvent-accessible surface area, and PCA. MDAnalysis integrates with NumPy, pandas, and matplotlib, making it the standard tool for post-simulation structural analysis in computational chemistry and drug discovery. ## When to Use - Computing RMSD and RMSF of protein backbone or specific residue groups after MD simulation - Analyzing ligand binding stability: pocket RMSD, contact persistence, hydrogen bond occupancy - Performing principal component analysis (PCA) on trajectory conformations - Computing solvent-accessible surface area (SASA), radius of gyration, and end-to-end distance - Extracting representative cluster structures from long MD trajectories for visualization …
Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/mdanalysis-trajectory@sha256:27f1651a8a6d6c0dThe line at the top of this page pins the label git:20260428.81ea2d2, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_qeos2fgvnd34mssy)
1 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 2 versions of this file, between Feb 18, 2026 and Apr 28, 2026, about one every 69 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260428.81ea2d2 latest | 2026-04-28 | 81ea2d2 | 14,272 B | A | view · diff |
| git:20260218.8df1694 | 2026-02-18 | 8df1694 | 14,386 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (14272 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
jaechang-hits/sciagent-skills · 381 stars · license a license file GitHub does not identify · pushed 2026-10-16 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_qeos2fgvnd34mssy GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/mdanalysis-trajectory GET https://markdownregistry.com/api/v1/blob/27f1651a8a6d6c0de4202c88aca8206436fa313eac2d25d1257f5a0112639a23
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.