Supported formats — Helix docs

Trajectories

Extension	From	Notes
.xtc	GROMACS	Compressed, lossy. Most common.
.trr	GROMACS	Full precision, includes velocities and forces.
.dcd	CHARMM / NAMD	Binary, common in NAMD and OpenMM exports.
.nc	AMBER	NetCDF, AMBER-flavoured.
.lh5	MDTraj	Lossy HDF5, compact for sharing.

Topologies

Extension	From	Notes
.pdb	Protein Data Bank	Universal but lossy. No bond orders.
.gro	GROMACS	Coordinates + residues, no bonds.
.psf	CHARMM / NAMD	Bonds and connectivity, pairs with .dcd.
.prmtop	AMBER	Full topology with charges and parameters.
.top	GROMACS	Force-field topology, pairs with .gro.
.cif	PDBx / mmCIF	Modern PDB, recommended for new uploads.

What gets indexed

When you upload a topology, our parser extracts:

Chain IDs and residue counts
Atom counts per chain and per residue type
Bond list (if available)
A thumbnail of frame 0
Estimated simulation length from the trajectory frame count

This metadata is what powers the search filters on /browse and the title bar on each simulation page.

Best practices

Strip waters and ions from the trajectory you upload — they bloat file size without adding interpretability. Keep them in a separate run if reviewers ask.
Use .xtc for the public version. .trrdoubles file size for fidelity most viewers won't notice.
Match the stride to the analysis you want viewers to do. 10 ps stride is the sweet spot for protein-scale dynamics; 1 ps for fast loops.
If your topology lacks bond information (e.g. plain PDB), the viewer will infer bonds by distance — usually fine but check the preview before publishing.

On the roadmap

Native support for OpenMM .datreporters and for streaming partial trajectories without a full download is in design. Open an issue if your engine produces something we don't list above.