Is io.github.wjgoarxiv/vmd-hydrate-mcp safe to use?

io.github.wjgoarxiv/vmd-hydrate-mcp has no known CVEs as of the latest MCPpedia security scan. It does not require authentication, so any local process can connect — keep this in mind in shared environments.

How do I install io.github.wjgoarxiv/vmd-hydrate-mcp?

io.github.wjgoarxiv/vmd-hydrate-mcp can be installed by cloning its GitHub repository and following the setup instructions in the README.

What AI clients work with io.github.wjgoarxiv/vmd-hydrate-mcp?

io.github.wjgoarxiv/vmd-hydrate-mcp is compatible with claude-desktop, cursor, claude-code. It uses stdio transport.

io.github.wjgoarxiv/vmd-hydrate-mcp

Drive VMD for GROMACS/LAMMPS analysis + clathrate-hydrate cage science (needs a local VMD)

GitHub

No known CVEs

No license

Maintenance unknown

No commit data

Works with most clients

Transport: stdio

0 tools

Token cost not measured

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Education

Step 1

Install in your client

Config is the same across clients — only the file and path differ.

Supported in Claude Desktopstdio · Node 18+

Paste into ~/Library/Application Support/Claude/claude_desktop_config.json

{
  "mcpServers": {
    "io-github-wjgoarxiv-vmd-hydrate-mcp": {
      "command": "<see-readme>",
      "args": []
    }
  }
}

Are you the author?

Add this badge to your README to show your security score and help users find safe servers.

Embed in your READMEAbout badges →

[![MCPpedia Score](https://mcppedia.org/api/badge/io-github-wjgoarxiv-vmd-hydrate-mcp)](https://mcppedia.org/s/io-github-wjgoarxiv-vmd-hydrate-mcp)

Read me

What io.github.wjgoarxiv/vmd-hydrate-mcp does

Drive VMD for GROMACS/LAMMPS analysis + clathrate-hydrate cage science (needs a local VMD)

Test This Server

No automated test available for this server. Check the GitHub README for setup instructions.

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Scored, not listed

Why this score

Five weighted categories — click any category to see the underlying evidence.

Score breakdown

0/100across 5 weighted dimensions

How we score →

0255075100

−100

Security

Maintenance

Efficiency

Documentation

Compatibility

Categoriesclick a row to see evidence

Security

OSV.dev

No known CVEs.

No package registry to scan.

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Frequently Asked Questions

Is io.github.wjgoarxiv/vmd-hydrate-mcp safe to use?: io.github.wjgoarxiv/vmd-hydrate-mcp has no known CVEs as of the latest MCPpedia security scan. It does not require authentication, so any local process can connect — keep this in mind in shared environments.
How do I install io.github.wjgoarxiv/vmd-hydrate-mcp?: io.github.wjgoarxiv/vmd-hydrate-mcp can be installed by cloning its GitHub repository and following the setup instructions in the README.
What AI clients work with io.github.wjgoarxiv/vmd-hydrate-mcp?: io.github.wjgoarxiv/vmd-hydrate-mcp is compatible with claude-desktop, cursor, claude-code. It uses stdio transport.

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Discussion

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Education

Step 1

Install in your client

Config is the same across clients — only the file and path differ.

Supported in Claude Desktopstdio · Node 18+

Paste into ~/Library/Application Support/Claude/claude_desktop_config.json

{
  "mcpServers": {
    "io-github-wjgoarxiv-vmd-hydrate-mcp": {
      "command": "<see-readme>",
      "args": []
    }
  }
}

Are you the author?

Add this badge to your README to show your security score and help users find safe servers.

Embed in your READMEAbout badges →

[![MCPpedia Score](https://mcppedia.org/api/badge/io-github-wjgoarxiv-vmd-hydrate-mcp)](https://mcppedia.org/s/io-github-wjgoarxiv-vmd-hydrate-mcp)

Read me

What io.github.wjgoarxiv/vmd-hydrate-mcp does

Drive VMD for GROMACS/LAMMPS analysis + clathrate-hydrate cage science (needs a local VMD)

Test This Server

No automated test available for this server. Check the GitHub README for setup instructions.

README

vmd-hydrate-mcp

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

Quick Start · Features · MCP Tools · Usage · 한국어

[!NOTE] An MCP server that lets Claude (or any MCP client) control VMD directly — load GROMACS/LAMMPS trajectories, identify clathrate-hydrate cages (sI/sII/sH), script headless renders, and compute order parameters (F3/F4) and H-bond networks — turning molecular-dynamics analysis into a conversation. Unlike the existing VMD MCP, it keeps a stateful VMD session, is secure by default, and owns the one thing no other MCP does: hydrate cage science.

See it in action

Every frame is a real headless VMD (Tachyon) render, driven entirely through the MCP server. The sII cages — 128 × 5¹² + 60 × 5¹²6⁴ — are identified by this repo, not mocked. · ▶ full-quality MP4

Features

Clathrate Cage Identification -- find and classify hydrate cages (5¹², 5¹²6², 5¹²6⁴, …) from the H-bond network and label the crystal structure (sI/sII/sH). Validated on the sII benchmark (128 small cages, exact).
Photorealistic, Style-by-Prompt Cage Rendering -- cages render with ambient occlusion + shadows, orthographic by default, each cage type in ONE unified color (a curated palette: 5¹²=cyan, 5¹²6⁴=red, …). Just ask: "show only the sII large cages in magenta with emphasized width" and the MCP filters, recolors, and thickens them.
Stateful VMD Session -- a persistent VMD process (Tcl socket server) keeps your molecules, selections, and camera alive across tool calls -- no reloading on every command.
Hydrate Order Parameters -- F3 (tetrahedrality) and F4 (⟨cos 3φ⟩) computed in pure NumPy, validated to the reference to 6 decimals (F4 = 0.926698 on the sII benchmark).
H-bond Networks -- water–water hydrogen-bond graph with coordination stats, the substrate for cage identification.
Headless Rendering -- CPU Tachyon ray-traced PNGs with no display or GPU, returned inline as images. Works on laptops, servers, and HPC.
Attended (GUI) Mode -- run fully offscreen (default), or set VMD_HYDRATE_MCP_DISPLAY=gui to open a visible VMD window and watch Claude load, color, rotate, and render your system live.
GROMACS + LAMMPS -- one server ingests .gro/.xtc/.trr, LAMMPS .data/dump, PDB, DCD, mmCIF.
Secure by Default -- filesystem allowlist + a Tcl command allowlist (not a bypassable denylist) + a loopback, token-gated control socket. No run_tcl foot-gun exposed.
MCP-Native -- clean English tool names and typed outputs; works in Claude Desktop, Claude Code, and any MCP client.

Quick Start

[!IMPORTANT] Requires a local VMD install (2.0b1 or 1.9.4+) — this server drives your VMD; no registry or package ships it. On macOS, VMD lives inside a .app, so set VMD_BIN if vmd isn't on your PATH. (The pure hydrate/measure tools still work without VMD.)

Install

Zero-install via uvx (recommended):

uvx vm

... [View full README on GitHub](https://github.com/wjgoarxiv/vmd-hydrate-mcp#readme)

Loading README…

Scored, not listed

Why this score

Five weighted categories — click any category to see the underlying evidence.

Score breakdown

0/100across 5 weighted dimensions

How we score →

0255075100

−100

Security

Maintenance

Efficiency

Documentation

Compatibility

Categoriesclick a row to see evidence

Security

OSV.dev

No known CVEs.

No package registry to scan.

Help improve this page

This server is missing a description. Tools and install config are also missing.If you've used it, help the community.

Add information

Community

Reviews

Be the first to review

Have you used this server?

Share your experience — it helps other developers decide.

How easy was setup?Did it work reliably?How was the documentation?

Frequently Asked Questions

Is io.github.wjgoarxiv/vmd-hydrate-mcp safe to use?: io.github.wjgoarxiv/vmd-hydrate-mcp has no known CVEs as of the latest MCPpedia security scan. It does not require authentication, so any local process can connect — keep this in mind in shared environments.
How do I install io.github.wjgoarxiv/vmd-hydrate-mcp?: io.github.wjgoarxiv/vmd-hydrate-mcp can be installed by cloning its GitHub repository and following the setup instructions in the README.
What AI clients work with io.github.wjgoarxiv/vmd-hydrate-mcp?: io.github.wjgoarxiv/vmd-hydrate-mcp is compatible with claude-desktop, cursor, claude-code. It uses stdio transport.