A molecular-dynamics trajectory can look like “just a file,” until it refuses to open—or opens without the result you expected. The file may contain a sequence of coordinates, while the molecular structure and topology are stored separately. And a format supported for reading is not necessarily supported for writing.
A quick check before you start can save time: identify the trajectory format, confirm whether SAMSON can read or write it, and check whether your workflow also needs a structure or topology file.
Read the columns, not just the file extensions
SAMSON’s supported-formats reference lists these molecular trajectory formats and their documented read/write support:
- Read and write: DCD, NC (AMBER NetCDF), PDB, TRR, and XTC.
- Read only: ARC, LAMMPSTRJ, TNG, TRJ, and XYZ.
This distinction matters when moving data between tools. For example, the reference lists XTC as both readable and writable, but lists TNG as readable only. If your next step requires exporting a trajectory, check the “Write” column before choosing an output format. The documentation also notes that SAMSON uses the chemfiles library to read and write some trajectory formats.
Know what the trajectory does—and does not—contain
A trajectory is a sequence of molecular configurations. It may not be a complete, standalone description of the system. In particular, the supported-formats page identifies PARM7 and PRMTOP as AMBER topology files used when loading AMBER NetCDF trajectories. That is a useful clue: for an AMBER NetCDF workflow, keep the topology file available alongside the trajectory rather than treating the trajectory as the only input.
Other formats can also represent different kinds of data. PDB appears in SAMSON’s lists for both molecular structures and trajectories. So the extension alone may not tell you what role a file plays in your project; consider how it was produced and what information it is meant to carry.
A simple pre-load checklist
- Check the extension and intended format. Match the file to the trajectory list rather than assuming that a familiar-looking extension has identical capabilities everywhere.
- Confirm the operation. Are you importing a trajectory, exporting one, or both? Read and write support are listed separately.
- Gather associated files. For AMBER NetCDF, note the documented use of PARM7 or PRMTOP topology files. Keep related files together so you can identify the correct inputs.
- Check aliases. The reference lists NCDF and NCTRAJ as read aliases for NC. If a file uses one of these names, the alias information may help you identify it.
- Plan the handoff. If the target application needs a format that SAMSON does not list as writable, choose an available export format that fits your next step, or investigate whether an extension provides the needed capability.
When the format you need is missing
The formats page describes its list as non-comprehensive: SAMSON Extensions may support additional formats. If you cannot find a needed format, you can ask about it on the SAMSON Connect Forum, or explore developing an importer or exporter using the importer and exporter documentation.
The takeaway is simple: verify the format, the direction of file support, and any companion files before building your workflow around a trajectory. See the original supported-formats reference for the complete list and details.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.