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Run LAMMPS from your agent

QuickMDSim 5 min read

The workbench loop was already short: project, input, run, log. It now lives on an authenticated MCP server, so the agent you already talk to can run that loop for you.

What this is

MCP (Model Context Protocol) is how an agent calls a remote tool the same way it calls a local one. QuickMDSim’s server exposes the jobs you already know — list projects, write input.lammps, submit, poll, read stdout.txt — behind a personal access token.

It is not a second product. Same account, same credits, same Cloudflare LAMMPS containers, same 1 / 2 / 4 core sizes. The browser app is still there when you want to watch a movie or poke at a dump.

Why it belongs here

A lot of LAMMPS time is not physics. It is “open the editor, paste the input, click Run, wait, download the log.” That is exactly the kind of loop an agent is good at, once it has a credential and a short list of tools.

The useful version is boring on purpose. No new force field. No “AI discovered a molecule.” You still write the input. The agent types it in, submits, and brings the log back.

Setup, end to end

  1. In the app, open Account. Create an API token. Copy the qmd_… secret — it is shown once.
  2. Point the client at https://quickmdsim-api.compoundhq.workers.dev/mcp with Authorization: Bearer qmd_….
  3. Ask the agent to check whoami, create a project, write a small input, and submit.

Copy-paste configs for Hermes, Claude Desktop, Claude Code, and Cursor live on the MCP docs page. If a call comes in without a token, the server answers 401 — there is no anonymous job path.

A first job

A 10-step Lennard-Jones quench is enough to prove the pipe. Create a project, overwrite the stub input.lammps, submit_job, then poll get_job until status_label is done. read_output on stdout.txt should show the usual LAMMPS banner.

Multi-file jobs work the same as in the app: write_file the potential (Al99.eam.alloy, a data.lammps, whatever pair_coeff names) into the same project. Do not pick the data file as the primary input.

What the token can and cannot do

  • It sees only your account. Another user’s project id returns not found.
  • Revoke it on the Account page; the next call is 401.
  • Email still has to be verified. Credits still have to be there.
  • Free stays on 1 core. Paid can pass vcpus 2 or 4.
  • Text logs and dump excerpts come back over MCP. Movies and snapshots stay in the app.

Where to start

Docs: quickmdsim.com/docs/mcp. App: Account → API tokens. The rest is an input you already know how to write.