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alterlab-molecular-dynamics

alterlab-molecular-dynamics is a skill for Claude Code from AlterLab-IEU/AlterLab-Academic-Skills. It costs 98 tokens per session (4,537 once invoked), scanned A, original, MIT.

A toolkit for simulating how proteins and small drug-like molecules move over time. It uses molecular dynamics, a computer method that models atomic motion, and analyzes the resulting movement data.

In plain words
What is it for?
Prepare protein or ligand systems, minimize their energy, run simulations, and analyze motion using measures such as structural change, flexible regions, contacts, and energy surfaces.
Why use it?
It helps researchers study molecular stability, interactions, and behavior that cannot be seen from a still structure alone.

Skill for Claude Code

Written for Claude Code: allowed-tools in frontmatter.

Part of the alterlab-cheminformatics plugin — 12 skills shipped together

not rated 85repo +3 changed yesterday A scan SkillSpector: pass 98 tokens original MIT

Good fit Prepare protein or ligand systems, minimize their energy, run simulations, and analyze motion using measures such as structural change, flexible regions, contacts, and energy surfaces.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/alterlab-ieu/alterlab-academic-skills/alterlab-molecular-dynamics
View source ↗ AlterLab-IEU/AlterLab-Academic-Skills alterlab-ieu.github.io
Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent
npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-molecular-dynamics
Clone the repo
git clone --depth 1 https://github.com/AlterLab-IEU/AlterLab-Academic-Skills

Made for: Claude Code.

Or install alterlab-cheminformatics, the plugin that ships this one along with the rest of its 12 skills.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for alterlab-molecular-dynamics

README.md
[![agentmods](https://agentmods.dev/badge/skills/alterlab-ieu/alterlab-academic-skills/alterlab-molecular-dynamics/github.svg)](https://agentmods.dev/skills/alterlab-ieu/alterlab-academic-skills/alterlab-molecular-dynamics)
Your own site
<a href="https://agentmods.dev/skills/alterlab-ieu/alterlab-academic-skills/alterlab-molecular-dynamics"><img src="https://agentmods.dev/badge/skills/alterlab-ieu/alterlab-academic-skills/alterlab-molecular-dynamics/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for alterlab-molecular-dynamics

Your own site · 80×15
<a href="https://agentmods.dev/skills/alterlab-ieu/alterlab-academic-skills/alterlab-molecular-dynamics"><img src="https://agentmods.dev/badge/skills/alterlab-ieu/alterlab-academic-skills/alterlab-molecular-dynamics.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 98 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 4,537 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe. Third-party audits
  • NVIDIA SkillSpector pass 7 Sept 2026
How audits are shown
Origin original No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00098 $0.04537
Opus 5.5 $0.00039 $0.01815
Sonnet 5.5 $0.00020 $0.00907
Haiku 4.5 $0.00010 $0.00454

Measured yesterday against content hash a771fb33045c, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

alterlab-molecular-dynamics scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured yesterday.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

skills/cheminformatics/alterlab-molecular-dynamics/SKILL.md · 491 lines

How it starts

The opening of the file, as written. The whole thing — 491 lines — stays where its author put it; the contents beside it link to each section on GitHub.

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

Installation (verified as of 2026-09: OpenMM 8.6.1, MDAnalysis 2.10, pdbfixer 1.12):

# uv (preferred) — all three publish binary wheels on PyPI, no conda needed
uv add openmm "mdanalysis>=2.10" pdbfixer
# If a pdbfixer wheel is unavailable for your platform, install from source:
uv pip install "pdbfixer @ git+https://github.com/openmm/pdbfixer.git"

# conda-forge alternative (pulls CUDA builds on Linux):
# conda install -c conda-forge openmm mdanalysis pdbfixer nglview

Note: on Apple Silicon there is no CUDA; OpenMM falls back to the CPU (and, on macOS, OpenCL/Metal) platforms — see the platform-selection block below.

When to Use This Skill

Use molecular dynamics when:

  • Protein stability analysis: How does a mutation affect protein dynamics?
  • Drug binding simulations: Characterize binding mode and residence time of a ligand
  • Conformational sampling: Explore protein flexibility and conformational changes
  • Protein-protein interaction: Model interface dynamics and binding energetics
  • RMSD/RMSF analysis: Quantify structural fluctuations from a reference structure
  • Free energy estimation: Compute binding free energy or conformational free energy
  • Membrane simulations: Model proteins in lipid bilayers
  • Intrinsically disordered proteins: Study IDR conformational ensembles

Does NOT Trigger

Scenario Use Instead
Predicting an initial protein–ligand binding pose (no dynamics) alterlab-diffdock
Quantum chemistry, pKa, or cloud AutoDock Vina docking scores alterlab-rowan
Predicting the protein structure to simulate (no experimental PDB) alterlab-alphafold or alterlab-boltz
Parameterizing a small-molecule force field only (OpenFF/GAFF), no simulation alterlab-rdkit for structure prep, then OpenFF (below)

Read the full file on GitHub · 491 lines

Files

What ships with it

2 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. yesterday Changed · +2 lines a771fb33045c
  2. 1mo ago Changed · +11 lines 72d97ba7e98c
  3. 2mo ago First seen · 478 lines · 98 tokens per session scan A 1bf337fbb485

Subscribe to this mod's changes

alterlab-molecular-dynamics is a skill published in the GitHub repository AlterLab-IEU/AlterLab-Academic-Skills (85 stars, last pushed yesterday), licensed MIT. It adds 98 tokens to every session and 4,537 once invoked, about $0.0004 per session on Opus 5.5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

Scientificacademic-researchanthropicbioinformaticsdata-scienceprompt-engineeringresearch-tools
Related

alterlab-molecular-dynamics compared with skills from other repositories

alterlab-molecular-dynamics next to 6 skills from other repositories
ModTypeStarsLast pushLicenceScanTokensWorks with
alterlab-molecular-dynamicsAlterLab-IEU/AlterLab-Academic-SkillsSkill85yesterdayMITA98Claude Code
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ob-hrm-scale-adaptorNero1688/claude-academic-skillsSkill1315d agoMITA318Claude Code, Codex
reproducibility-architectNero1688/claude-academic-skillsSkill1315d agoMITA521Claude Code, Codex
thesis-consistency-auditNero1688/claude-academic-skillsSkill1315d agoMITA500Claude Code, Codex
journal-submission-scoutNero1688/claude-academic-skillsSkill1315d agoMITA479Claude Code, Codex