Koskamo

vmd-hydrate-mcp

An MCP server that drives VMD for GROMACS/LAMMPS trajectory analysis and clathrate-hydrate cage science. It allows agents to load molecular dynamics trajectories, identify hydrate cage structures, compute order parameters, and generate headless photorealistic renders via a stateful VMD session.

Package and access

Local package with source-attributed installation metadata. Koskamo does not execute packages during review.

vmd-hydrate-mcp logo, by wjgoarxivCommunity listingLocal stdioSource reviewed; not executedPublished by wjgoarxiv
You need:Requires a local VMD install (2.0b1 or 1.9.4+)
Vendor documentation

What you can do with it

  • Identify and classify clathrate hydrate cages (sI/sII/sH) from H-bond networks
  • Render photorealistic, style-by-prompt images of hydrate cages using headless VMD
  • Compute hydrate order parameters (F3/F4) and analyze H-bond networks
  • Load and analyze GROMACS and LAMMPS trajectory files

Source and maintenance

Community listingRegistry 0.2.0
mcp-registry: io.github.wjgoarxiv/vmd-hydrate-mcp@0.2.0Source repository
Maintenance checked

Packages and installation

Source-provided package data. Koskamo has not executed or live-probed this package.

vmd-hydrate-mcp 0.2.0

pypi
vmd-hydrate-mcp package definition
{
  "version": "0.2.0",
  "transport": "stdio",
  "identifier": "vmd-hydrate-mcp",
  "registryType": "pypi"
}

Tools

Reported by the attributed source; not independently observed by Koskamo.

No tool definitions available.

Connect from your client

Each snippet configures the same source-provided package; replace placeholders before use.

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Cursor

Merge this local stdio configuration, replace every placeholder environment value, and restart Cursor. Koskamo has not executed this package.
Cursor configuration
{
  "mcpServers": {
    "vmd-hydrate-mcp": {
      "command": "uvx",
      "args": [
        "vmd-hydrate-mcp==0.2.0"
      ]
    }
  }
}

Cline

Merge this local stdio configuration, replace every placeholder environment value, and restart Cline. Koskamo has not executed this package.
Cline configuration
{
  "mcpServers": {
    "vmd-hydrate-mcp": {
      "command": "uvx",
      "args": [
        "vmd-hydrate-mcp==0.2.0"
      ]
    }
  }
}

VS Code

Merge this local stdio configuration, replace every placeholder environment value, and restart VS Code. Koskamo has not executed this package.
VS Code configuration
{
  "servers": {
    "vmd-hydrate-mcp": {
      "type": "stdio",
      "command": "uvx",
      "args": [
        "vmd-hydrate-mcp==0.2.0"
      ]
    }
  }
}

Claude Desktop

Merge this local stdio configuration, replace every placeholder environment value, and restart Claude Desktop. Koskamo has not executed this package.
Claude Desktop configuration
{
  "mcpServers": {
    "vmd-hydrate-mcp": {
      "command": "uvx",
      "args": [
        "vmd-hydrate-mcp==0.2.0"
      ]
    }
  }
}

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