Molecular-Dynamics Trajectories
Load a topology and trajectory, verify the system, control playback, and inspect frames reliably.
A trajectory is a sequence of molecular coordinate frames. The topology identifies the atoms and bonds; the trajectory supplies their changing positions. The files must describe the same atom set in the same order.
An active trajectory is marked with TRAJ under Structures. Playback, frame position, and speed controls appear along the bottom of the Viewer; Enhanced precision confirms the detailed paused or slow-playback state.
What this example shows
The active topology contains the protein, ligand, lipids, ions, hydrogens, and water. The bottom
bar reports the current frame and total frame count, while the speed control determines how fast
the sequence advances.
Before you load
Confirm that you have:
- A supported topology, commonly PDB, mmCIF, or GRO.
- A compatible trajectory, such as XTC, TRR, or DCD.
- The correct pair for the same simulation system.
A topology and trajectory can both be valid files and still be incompatible with each other. Atom count and atom order must match.
Load from your computer
See Supported File Formats for accepted combinations.
Validate the loaded system
Before interpreting motion, check:
- The expected number of frames is shown.
- The topology contains the expected protein, ligand, lipid, ions, and water.
- Bonds and components do not look obviously corrupted.
- The system remains coherent when you scrub through several separated frames.
- The active structure is the trajectory, not another static structure loaded alongside it.
If the Viewer reports an atom-count or pairing error, stop and identify the correct topology rather than retrying the same pair.
Playback controls
When a trajectory is active, the bottom playback bar provides:
- Play / Pause for continuous playback.
- A frame slider for direct scrubbing.
- The current frame and total frame count, for example 88 / 1750.
- A speed control from very slow inspection to faster overview playback.
Review motion deliberately
Detail modes
When the loading workflow offers detail choices, they trade startup speed against frame coverage.
| Mode | What it provides | Use it for |
|---|---|---|
| Preview | A quick, strided sample | Fast orientation and file validation |
| Representative | A selected subset of diverse frames | Broad conformational review with reduced data |
| Full | Every available frame | Frame-level analysis and complete playback |
Start with Preview when you need a fast first look. Use Full when every frame matters. Do not compare frame numbers between a subsampled mode and the full trajectory without checking how the subset maps to the source.
Large systems and precision
The Viewer adapts playback for large systems. During faster motion, solvent or other high-volume detail may be optimized to preserve responsiveness. When paused or moving slowly, an Enhanced Precision indicator may show that exact per-frame detail is active.
Pause before inspecting solvent placement, measuring geometry, or capturing a publication image. Smooth playback is for temporal orientation; a paused frame is the reliable state for detailed inspection.
Analyze the trajectory
Use Applications → MD → Analysis after the trajectory is loaded and active. For spatial contacts, open Interactions and confirm whether the current analysis is frame-specific or summarizes a range.
Measurements remain anchored across frames, which makes them useful for following a changing distance, angle, or torsion. Save important states as viewer sessions or story scenes with the frame context in the name or description.