Run Molecular Dynamics in Claude with SimAtomic MCP

You can run molecular dynamics (MD) simulations from Claude by connecting the SimAtomic MCP server at https://mcp.simatomic.com/mcp. Claude uses SimAtomic tools to upload prepared inputs, submit simulation jobs, monitor progress, and retrieve results. SimAtomic performs the compute on remote GPUs; Claude helps organize the workflow and analyze the outputs.

Simulations run remotely on modern GPUs. Jobs can run in parallel, and SimAtomic provides dedicated GPUs for teams that need dedicated compute capacity. Contact us about dedicated GPUs.

1. Use Claude Desktop in Code mode

For this workflow, use the Claude Desktop app and select Code mode (the </> button, callout 1 below). With a local project folder, Claude can write and save analysis scripts, run them with your installed tools, and download results directly into your workspace. This keeps inputs, scripts, trajectories, and plots together for later reuse. Get Claude Desktop and check Code access requirements.

In the desktop app, open Customize → Connectors (callouts 2 and 3), then click Add (callout 4) to open the custom connector form. Older versions may show this under Settings → Connectors → Add custom connector. If SimAtomic is already listed, open it and skip to step 3.

2. Add SimAtomic

Enter the following details in the custom connector form:

Click Continue and follow the remaining setup prompts. If advanced OAuth client fields appear, leave them empty unless SimAtomic has supplied specific values.

3. Connect your account

Choose Connect if prompted, then sign in on the SimAtomic screen. Review the requested access and approve it to finish linking your account. Back in Claude, open SimAtomic’s details: a Disconnect button and the tool list indicate an active connection. Set Submit job to Needs approval so you can review each submission.

On a Team or Enterprise account, an organization owner may need to add SimAtomic before members can connect. See Claude’s custom connector guide for the current account and setup requirements.

4. Create a local project folder

After connecting SimAtomic, click the + beside the Projects section heading in the sidebar (callout 5 in the first image). Create a new project and connect it to a local folder, such as SimAtomic-study. Open that project, use Code mode, and work from its local folder.

Place your input structures in that folder and work from the same project for setup, job monitoring, downloads, and analysis. Local mode gives Claude access to your working files; SimAtomic simulations still run on remote GPUs. Claude can save its analysis scripts and downloaded outputs in the selected folder.

5. Check the connection

In your new local Code session, open + → Connectors beside the prompt box and check that SimAtomic is available. Paste this prompt:

Prompt: What tools are available through my SimAtomic connector? Explain what I can do with them without submitting a job.

Look for tools such as List my jobs, Get job status, Submit job, and Get result url. You can also ask Claude to list your existing jobs to verify account access without starting new compute work.

6. Try your first workflow

Save your prepared structure in the project folder, then reference its filename in your prompt and ask Claude to check the input and plan a short test:

Prompt: Use SimAtomic to check [input filename] in this project folder and prepare a short MD test. Show me any input issues, the proposed simulation settings, and the estimated runtime and credits if available. Wait for my confirmation before uploading or submitting anything.

Review the structure preparation and settings, resolve any issues, then confirm the run. If the connector needs a prepared archive or another upload route, have Claude explain the required format before proceeding.

Save the job ID Claude returns. You can use it to follow up:

Prompt: Check the status of SimAtomic job [job ID]. If it has finished successfully, download the results into this project folder and explain the output files. Save any analysis scripts you create in a scripts subfolder and their plots in an analysis subfolder.

7. See a complete Claude simulation session

The interactive example below shows the full workflow together: Claude checks and repairs an unsupported input, asks for confirmation before submission, follows the remote GPU job, summarizes the results, and opens the completed trajectory beside the chat. The trajectory viewer includes frame controls, temperature, Cα RMSD, RMSF, potential-energy drift, contacts, and simulation metadata.

Open the full Claude session demo →

This is a condensed example session and demonstration trajectory. Use the results from your own SimAtomic job for scientific interpretation.

If something doesn’t connect

• Cannot add a connector? Check your Claude plan’s connector allowance or ask your workspace owner to add SimAtomic.
• Connection or authentication error? Check the full HTTPS URL, then reconnect and complete the authentication flow.
• Claude cannot see the tools? Check the connector in Customize → Connectors, then start a new Code session in your local project folder.
• A job fails? Ask for the returned error and check the input and account credits before resubmitting.