molecular-dynamics SKILL.md skillA
molecular-dynamics from k-dense-ai/scientific-agent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add k-dense-ai/scientific-agent-skills/molecular-dynamics@v1.3Pins v1.3 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- k-dense-ai/scientific-agent-skills
- Path
skills/molecular-dynamics/SKILL.md- Versions recorded
- 6
- Latest version
- v1.3, committed Oct 1, 2026
- First version recorded
- Jun 11, 2026
- Size
- 18,971 bytes
- Repository stars
- 56,497
- License
- MIT
Runs and analyzes molecular dynamics simulations with OpenMM and MDAnalysis. Sets up protein/small molecule systems, defines force fields, runs energy minimization and production MD, and analyzes trajectories (RMSD, RMSF, contact maps, free energy surfaces). For structural biology, drug binding, and biophysics.
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
# Molecular Dynamics ## Overview Molecular dynamics (MD) simulation computationally models the time evolution of molecular systems by integrating Newton's equations of motion. This skill covers two complementary tools: - **OpenMM** (https://openmm.org/): High-performance MD simulation engine with GPU support, Python API, and flexible force field support - **MDAnalysis** (https://mdanalysis.org/): Python library for reading, writing, and analyzing MD trajectories from all major simulation packages **Reviewed versions:** OpenMM 8.6.1 and MDAnalysis 2.10.0. Reference-platform smoke checks use small synthetic systems; GPU performance and scientific convergence are not established by them. OpenMM latest API pages identify a development build, so the installed 8.6.1 API is the executable reference. **Installation into a dedicated environment:** ```bash uv venv --python 3.12 .venv-md uv pip install --python .venv-md/bin/python "openmm==8.6.1" "MDAnalysis==2.10.0" matplotlib pandas # Windows: use .venv-md/Scripts/python.exe instead ``` ## When to Use This Skill Use molecular dynamics when: - **Protein stability analysis**: How does a mutation affect protein dynamics? …
Read the whole file at its exact version.
How to install
mdr add k-dense-ai/scientific-agent-skills/molecular-dynamics@sha256:1efb31165ec1477bThe line at the top of this page pins the label v1.3, 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_vb2uxl3iavsxoqsg)
4 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 6 versions of this file, between Jun 11, 2026 and Oct 1, 2026, about one every 22 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| v1.3 latest | 2026-10-01 | a92663a | 18,971 B | A | view · diff |
| v1.2 | 2026-09-30 | ce9e6e9 | 15,761 B | A | view · diff |
| v1.1 | 2026-07-31 | 4226ca8 | 14,721 B | A | view · diff |
| v1.0 | 2026-07-31 | bd99c01 | 14,721 B | A | view · diff |
| v1.0 | 2026-07-26 | b085e11 | 14,715 B | A | view · diff |
| git:20260611.1b8fae3 | 2026-06-11 | 1b8fae3 | 14,720 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 (18971 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
k-dense-ai/scientific-agent-skills · 56,497 stars · license MIT · pushed 2026-11-02 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_vb2uxl3iavsxoqsg GET https://markdownregistry.com/api/v1/resolve?ref=k-dense-ai/scientific-agent-skills/molecular-dynamics GET https://markdownregistry.com/api/v1/blob/1efb31165ec1477b37c31394ba04b5fb280d44db8907afdf2a956e48487f1136
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.