MDEngine — Claude Code MCP server for molecular dynamics
Inspect trajectories and run LAMMPS jobs from your agent: 13 analysis tools, Metal rendering, hosted GPU runs.
claude mcp add --transport http mdengine https://api.forcefieldsilicon.com/mcpWhat MDEngine 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.
What it helps with
- 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 for the agent
- How many frames and atoms are in
lj_melt.xyz? - Render a video from this trajectory with a cinematic orbit
- Submit
fe_oxidation.inas a background job and show me the log tail
How to install MDEngine
Platform CLI: remote server
claude mcp add --transport http mdengine https://api.forcefieldsilicon.com/mcpPlatform CLI: remote server
codex mcp add mdengine --url https://api.forcefieldsilicon.com/mcpConfig file
{
"mcpServers": {
"mdengine": {
"url": "https://api.forcefieldsilicon.com/mcp"
}
}
}Config file
{
"servers": {
"mdengine": {
"type": "http",
"url": "https://api.forcefieldsilicon.com/mcp"
}
}
}Platform CLI: remote server
gemini mcp add -t http mdengine https://api.forcefieldsilicon.com/mcpStep by step, with commands for each platform: How to add an MCP server to Claude Code, Codex, Cursor, VS Code, Gemini CLI and more
Questions about MDEngine
How do I install MDEngine in Claude Code?
Run claude mcp add --transport http mdengine https://api.forcefieldsilicon.com/mcp, then type /mcp, pick mdengine-cloud and authenticate.
What does MDEngine do?
It inspects molecular-dynamics trajectories, renders frames and video, and runs LAMMPS jobs — synchronously for short tests or detached for long ones.
Do I need LAMMPS installed?
Only for run and submit_lammps. Trajectory analysis and rendering work without it, and on the hosted tier the calculation runs on the provider's GPU.
