Work with Claude
Add the MCP connector, connect a local project folder, and prepare, run, and analyze simulations through a conversation.
Claude setup with screenshots →SimAtomic documentation
Molecular simulation.
Choose your workflow.
Run molecular dynamics on SimAtomic’s remote GPUs from Claude, Codex, or your own Python scripts. Start with a setup guide, then use the scientific reference to check your system and choose the settings.
Work with Codex
Connect SimAtomic in the desktop interface. Keep input files, downloaded trajectories, and analysis scripts together.
Codex setup with screenshots →Build your workflow
Upload an input archive, submit a job, poll its status, and retrieve results from a reproducible script.
Python and API workflow →One compute service, three ways to use it
Claude and Codex coordinate the workflow through Model Context Protocol (MCP). The API gives scripts direct access to job submission and results. SimAtomic performs the simulation; your assistant or script can download outputs and run additional analysis locally.
Jobs can run in parallel, subject to available compute capacity and credits. Contact SimAtomic for API access, compute packages, or dedicated GPU capacity. Your Claude or ChatGPT usage is billed separately from SimAtomic compute credits. See pricing and billing.
Check the science before the first run
Current preparation scope: a standard soluble protein, optionally with one chemically valid, posed 3D small-molecule SDF, in explicit water.
The automated pipeline repairs ordinary missing protein atoms, assigns receptor protonation, adds solvent and ions, parameterizes the system, and runs minimization, equilibration, and production MD. It does not fetch a structure, dock a ligand, rebuild an entire missing domain, or repair unsupported chemistry.
Capabilities, supported systems, and limitations →
Simulation parameters and defaults →
Connect an assistant through MCP
Server: https://mcp.simatomic.com/mcp
Transport: Streamable HTTP
Authorization: complete the sign-in flow with your SimAtomic API key.
Use the desktop setup guide for your client. The Codex guide uses a ChatGPT account in Codex; it does not configure ChatGPT on the web. Other MCP clients need compatible remote transport and authentication.
Prompt: What tools are available through my SimAtomic connector? Explain what I can do with them without submitting a job. Show the accepted input formats and simulation parameters.
See the complete workflow
Explore a Claude conversation alongside a trajectory viewer. The 5 ps example demonstrates the workflow; it is too short to establish convergence or biological conclusions.
API documentation
The Python/API workflow remains available, including simulation, trajectory analysis, optional MM/PBSA processing, input archives, status polling, and downloads.
Need help with your first system?
Email info@simatomic.com with the system type and scientific question. Check the support matrix before submitting systems with metals, cofactors, membranes, nucleic acids, or nonstandard residues.