Uploading a simulation
The upload form is one page. This walkthrough explains every field, what gets parsed automatically, and what reviewers look for.
What you'll need
- A trajectory file in one of the supported formats (see Supported formats).
- A topology file with atom names, residues, and bonds. Optional but strongly recommended — without it the viewer falls back to a generic stick representation with no chain colouring.
- A short description: force field, integrator, conditions, total simulated time, any citations.
Walking through the form
Open /upload and drag your trajectory file onto the top drop zone. The form will check the extension and refuse anything it can't read. Drop your topology in the second zone.
Name— a short title that helps people find your work when searching. We recommend starting with the system itself ("Spike protein RBD with ACE2") rather than the lab name or run number.
Description— this is where reviewers and the AI guide get their context. Include the force field, water model, ensemble, temperature, salt concentration, and length of the simulation. If there's a published paper, link it.
Category — the rough biological domain. Surfaces your simulation in the matching tile on the browse page.
Tags — free-text, comma-separated. Use these for engine names ( gromacs, amber, namd), force fields, methods (e.g. metadynamics), and simulation length.
License— defaults to CC BY 4.0 because most scientists want attribution-only reuse. CC0 if you don't care. CC BY-NC for non-commercial only. "Custom" lets you specify the terms in your description; reviewers will check the wording.
Visibility — Public is indexed and crawled. Unlisted is only reachable via the URL. Private is you and collaborators you add later from the simulation page.
After you submit
- The trajectory and topology are uploaded to object storage.
- A worker parses the topology to extract chains, residue counts, atom counts, and a thumbnail of frame 0.
- For public uploads, a reviewer checks that the description matches the data and that the license is consistent. Most reviews complete within 24 hours.
- Once approved, your simulation appears on browse. You'll get an email with the canonical URL.
Preview only