Sirius features full support for visualization of molecular dynamics trajectories. The formats include AMBER and CHARMM parameter and coordinate/trajectory files, including direct loading of compressed and consecutive files from the same simulation. For multiple input files, the user has an option to edit the order of files to ensure proper playback. Trajectory files that contain explicit solvent molecules may be loaded with or without solvent.

RMSD can be computed with respect to the first frame of the run or another structure of the same molecule that can be selected by the user. In addition, RMSD can be calculated for various subsets of the atoms: only heavy atoms, all atoms except solvent, protein/DNA backbone atoms, etc. A user-defined subset of atoms can also be used for RMSD calculation. In this case, changes within a specific part of the structure can be tracked.

For AMBER simulations, out files can be loaded directly. They are parsed for parameter and trajectory file locations, which are loaded automatically. In addition, energy values from the out files can be plotted as a graph. Both energy and RMSD graphs have a sliding marker that indicates the current position of playback within the overall trajectory. In addition, data can be exported as either an image or a text file.

Sirius reads binary DCD files, including those that contain bounding box and charge data. In the latter case, charges are read and can be displayed either by color or numeric atom labels.

PDB files can be used as parameter files, in addition to prmtop (AMBER) and PSF (CHARMM) files.