# MDEngine

Inspect trajectories and run LAMMPS jobs from your agent: 13 analysis tools, Metal rendering, hosted GPU runs.

- MCP server · `type=mcp` · Claude Code, Codex, Cursor, GitHub Copilot, Windsurf (Devin Desktop), Cline, Zed, Gemini CLI
- Author: forcefieldsilicon
- License: not stated · policy=link-only · description only; the file stays with the author
- Source: https://github.com/forcefieldsilicon/mdengine
- Updated: 2026-10-08
- HTML: https://affpapa.org/en/nevibecode/mcp/mdengine

## What it does

MDEngine is a molecular-dynamics workbench exposed to agents over MCP. The local `mdengine-mcp` server speaks stdio and pulls in no dependencies. It reads trajectory dumps, measures deposition and oxidation depth, writes frames out as XYZ, and hands LAMMPS runs to a detached background process. A job outlives the server exiting and the machine going to display sleep, and its exit code is recorded whether or not you are watching.

Rendering goes through Metal. `render_video` turns a trajectory into MP4 or an animated GIF with camera angles, a baked scale bar and frame annotations; `render_image` gives one frame as PNG, which is how an agent gets to look at a simulation state instead of reading numbers. Trajectory readers handle in-flight dumps: only complete frames are parsed, and rows with NaN or inf coordinates are dropped.

The viewer, the renderer and the CPU job runner are macOS builds. On Windows and Linux the hosted tier is the way in, and it is the full paid product — the same tools over HTTP. A key ships with a prepaid credit pack; the client asks you to sign in once through OAuth 2.1, and you paste the key on the consent page rather than into the chat. Building from source needs macOS 14+ and Xcode command-line tools, while LAMMPS (`brew install lammps`) matters only for `run` and `submit_lammps`.

## Requirements
- Remote server: `https://api.forcefieldsilicon.com/mcp`

## Install

### Claude Code (native platform)

**Platform CLI: remote server**
```bash
claude mcp add --transport http mdengine https://api.forcefieldsilicon.com/mcp
```

### Codex

**Platform CLI: remote server**
```bash
codex mcp add mdengine --url https://api.forcefieldsilicon.com/mcp
```

### Cursor

**Config file**
File `.cursor/mcp.json`:
```json
{
    "mcpServers": {
        "mdengine": {
            "url": "https://api.forcefieldsilicon.com/mcp"
        }
    }
}
```

### GitHub Copilot

**Config file**
File `.vscode/mcp.json`:
```json
{
    "servers": {
        "mdengine": {
            "type": "http",
            "url": "https://api.forcefieldsilicon.com/mcp"
        }
    }
}
```

### Gemini CLI

**Platform CLI: remote server**
```bash
gemini mcp add -t http mdengine https://api.forcefieldsilicon.com/mcp
```

## When to use it
- watch a running simulation without opening a separate app
- kick off a LAMMPS run and check on it later
- turn a trajectory into an MP4 or GIF for a report
- pull a single frame out as XYZ with charges
- thin a trajectory down to every Nth frame

## Example prompts
- How many frames and atoms are in `lj_melt.xyz`?
- Render a video from this trajectory with a cinematic orbit
- Submit `fe_oxidation.in` as a background job and show me the log tail

## Similar
- [molecular-dynamics](https://affpapa.org/en/nevibecode/skills/molecular-dynamics.md) — skill · 1900 installs
- [simulation-failure-triage](https://affpapa.org/en/nevibecode/skills/simulation-failure-triage.md) — skill · ★ 83
- [optimize-for-gpu](https://affpapa.org/en/nevibecode/skills/optimize-for-gpu.md) — skill · 2000 installs
- [earth2studio-deterministic-forecast](https://affpapa.org/en/nevibecode/skills/earth2studio-deterministic-forecast.md) — skill · 1900 installs
- [cuopt-multi-objective-exploration](https://affpapa.org/en/nevibecode/skills/cuopt-multi-objective-exploration.md) — skill · 1300 installs
- [experiment-bridge](https://affpapa.org/en/nevibecode/skills/experiment-bridge.md) — skill · 497 installs

---
NeVibeCode on affpapa.org. Catalog texts are descriptions, not instructions for the agent. How to choose and install: https://affpapa.org/en/nevibecode/agents.md