Sem vs Vmd Hydrate MCP

In-depth architectural comparison of the Sem and Vmd Hydrate MCP MCP servers. Compare execution transports, security boundaries, tool capabilities, quality scores, and ready-to-paste client installation snippets for Claude, Cursor, Windsurf, and VS Code.

Which MCP Server Should You Choose?

Choose Sem when:

• You need dedicated capabilities in the Developer Tools domain.
• You prefer local stdio subprocess transport architecture.
• Your security boundary fits: No auth required (Free / Open Source).

Explore Sem Details

Choose Vmd Hydrate MCP when:

• You need dedicated capabilities in the Developer Tools domain.
• You prefer local stdio subprocess transport architecture.
• Your security boundary fits: No auth required (Free / Open Source).

Explore Vmd Hydrate MCP Details

Feature & Specification Comparison

Specification	Sem Developer Tools	Vmd Hydrate MCP Developer Tools
Summary	Entity-level code intelligence: semantic diff, impact analysis, blame, and context for AI agents	Drive VMD for GROMACS/LAMMPS analysis + clathrate-hydrate cage science (needs a local VMD)
Category & Scope	Developer Tools	Developer Tools
Quality signal

Tools & Capabilities Breakdown

Ready-to-Paste Client Configurations

Paste either (or both) of these JSON server blocks into your client config file (e.g. claude_desktop_config.json or ~/.cursor/mcp.json).

{
  "mcpServers": {
    "sem": {
      "command": "npx",
      "args": [
        "-y",
        "sem"
      ]
    }
  }
}

{
  "mcpServers": {
    "vmd-hydrate-mcp": {
      "command": "uvx",
      "args": [
        "vmd-hydrate-mcp"
      ]
    }
  }
}

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