A molecular trajectory can be the most valuable record from a simulation—and the easiest file to mis-handle. You may know the filename extension but still need to answer two practical questions before choosing a workflow: can SAMSON read it, and can it write it? Those answers differ by format. The supported-formats reference makes that distinction explicit, which helps avoid a frustrating round of trial and error.
Here’s a quick guide to the trajectory formats listed for SAMSON, organized by what the documentation says about reading and writing:
- Read and write: DCD, NC (AMBER NetCDF), PDB, TRR, and XTC.
- Read listed; write not listed: ARC, LAMMPSTRJ, TNG, TRJ, and XYZ.
“Write not listed” is the useful distinction here: the reference does not indicate export support for those formats. If you need to bring a trajectory into SAMSON and later save it in another format, start with a format marked for both reading and writing rather than assuming that importing a file means it can also be exported.
Check the format in context
Some extensions are shared by different kinds of files. PDB, for example, appears in the documentation under both molecular structures and molecular trajectories. The extension alone therefore does not tell you whether a particular file represents a structure or a trajectory; use the file’s origin and intended contents to identify it.
For an AMBER NetCDF trajectory, pay attention to the topology file as well. The reference lists NC as the AMBER NetCDF format and notes that PARM7 or PRMTOP is used when loading AMBER NetCDF trajectories. In practice, that means you should identify the trajectory and its associated topology before starting, rather than treating the trajectory filename as the only piece of information you need.
A small pre-import checklist
- Identify the data type. Is the file a molecular structure or a trajectory? The reference documents those categories separately.
- Match the extension. Find the format in the molecular-trajectories list. Remember that aliases are noted for some formats: NC can also be called NCDF or NCTRAJ.
- Check the intended direction. Confirm whether you need to read the file, write one, or both. The table’s Read and Write columns are not interchangeable.
- Gather companion files. For AMBER NetCDF, check for the associated PARM7 or PRMTOP topology file.
- Keep the original. If you are testing an import or conversion, retain an untouched copy of the simulation output until you have checked the result.
One more useful detail: SAMSON uses the chemfiles library to read and write some trajectory formats. The documentation does not specify that every listed trajectory format is handled through that library, so treat it as context—not as a guarantee about any particular format.
When a format is missing or does not meet your needs, the documentation points to SAMSON importers and exporters as another route; extensions may also support additional formats beyond this non-comprehensive list. For the complete tables and format notes, see the SAMSON supported formats reference.
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