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Submit cloud LAMMPS jobs from an agent (MCP)

QuickMDSim 5 min read

The browser loop is project, input, run, log. The same loop is available over MCP (Model Context Protocol): an HTTP interface that lets a language-model client call named tools instead of clicking the UI.

What the server does

Tools cover list/create project, write input.lammps, submit, poll, and read stdout.txt. Authentication is a personal access token (qmd_…) or OAuth 2.1 with PKCE. There is no anonymous path; a missing credential returns HTTP 401.

It is the same account, credits, containers, and 1 / 2 / 4 CPU cores as the app. GPU (KOKKOS, NVIDIA L4) remains Pro-only, same as in the browser. Movies stay in the app; MCP returns text logs and dump excerpts.

Why

A large fraction of LAMMPS wall-clock on a laptop is typing, waiting, and fetching the log. An agent can do that once it has a credential and a short tool list. You still write the physics. The client does not invent a force field.

Setup

  1. In the app, open Account. Create an API token. Copy the qmd_… secret (shown once).
  2. Point the client at https://api.quickmdsim.com/mcp with Authorization: Bearer qmd_…. Grok-style connectors that require OAuth: client id quickmdsim-mcp, blank secret, PKCE only. Endpoints are on the MCP docs.
  3. Ask the client to call whoami, create a project, write a small input, and submit.

Config snippets for Hermes, Claude, and Cursor are on quickmdsim.com/docs/mcp.

A first job

A 10-step Lennard-Jones quench is enough to test the pipe. Overwrite the stub input.lammps, submit_job, poll get_job until status_label is done, then read_output on stdout.txt for the LAMMPS banner.

Multi-file jobs match the app: write the potential (Al99.eam.alloy, a data.lammps topology file, whatever pair_coeff names) into the same project. Do not mark the data file as the primary input.

Limits

  • A token sees only that account.
  • Revoke it on Account; the next call is 401.
  • Email must be verified. Credits must be present.
  • Free is 1 CPU core. Paid CPU can pass vcpus 2 or 4.

Docs: quickmdsim.com/docs/mcp. App: Account.