# vmd-hydrate-mcp

> vmd-hydrate-mcp — wjgoarxiv-vmd-hydrate-mcp. Use this tool when you need to analyze molecular dynamics simulations, specifically clathrate-hydrate cages, and render trajectories from GROMACS or LAMMPS files. It integrates with any Large Language Model (LLM) through the Model Context Protocol (MCP) to drive Visual Molecular Dynamics (VMD) for in-depth analysis. This tool is ideal for researchers and scientists working with molecular simulations who require a streamlined workflow for trajectory rendering and cage analysis.

Canonical page: https://skillsregistry.net/skills/wjgoarxiv-vmd-hydrate-mcp  
JSON: https://api.skillsregistry.net/v1/skills/wjgoarxiv-vmd-hydrate-mcp

## Description

Drive VMD from any LLM — render GROMACS/LAMMPS trajectories and analyze clathrate-hydrate cages through the Model Context Protocol.

## Trust

- **Trust score (0–1):** 0.68
- **Verification tier:** scanned
- **Last scanned:** 2026-08-29

## Facts

- **Version:** 1.0.0
- **Skill type:** atomic
- **Execution layer:** mcp-remote
- **Runtime environment:** api
- **Category:** ai-ml
- **Updated:** 2026-08-29

## Source

- **Source listing:** [Glama](https://glama.ai/mcp/servers/vplvqjswtk)
- **Repository:** <https://github.com/wjgoarxiv/vmd-hydrate-mcp>

## Use it

Resolve this record through the SkillsRegistry MCP server (no auth, read-only):

```
claude mcp add --transport http --scope user skillsregistry https://api.skillsregistry.net/mcp
```

```json
{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "get_skill",
    "arguments": {
      "slug": "wjgoarxiv-vmd-hydrate-mcp"
    }
  }
}
```

REST: `GET https://api.skillsregistry.net/v1/skills/wjgoarxiv-vmd-hydrate-mcp` · pull for local use: `GET https://api.skillsregistry.net/v1/skills/wjgoarxiv-vmd-hydrate-mcp/pull`

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SkillsRegistry indexes agent skills from public registries and GitHub. Skills we have analysed are scanned with Circle-IR and scored on six dimensions; each listing states its scan coverage. More: https://skillsregistry.net/llms.txt