A molecular dynamics trajectory can be perfectly valid and still be frustrating to work with: the file may open in one application but not another, or it may appear without the structural context you expected. Before troubleshooting the simulation itself, check two things: what kind of file you have, and whether you are handling a structure or a trajectory.
In SAMSON, these are separate format categories. A molecular structure describes a molecular system, while a trajectory contains changing coordinates over time. The supported-formats reference lists both categories, including which formats SAMSON can read and which it can write. That distinction is useful when planning a workflow: support for importing a format does not necessarily mean it can also be exported.
Start with the file extension
SAMSON lists several molecular trajectory formats. The table below is a quick guide to the formats named in the documentation:
- DCD: a binary trajectory used by CHARMM, NAMD, or LAMMPS. SAMSON can read and write it.
- NC: AMBER NetCDF format, also known for reading as NCDF or NCTRAJ. SAMSON can read and write it.
- XTC: a compressed GROMACS trajectory. SAMSON can read and write it.
- TRR: a GROMACS trajectory. SAMSON can read and write it.
- PDB: supported as a trajectory format, as well as a molecular-structure format. SAMSON can read and write it.
- ARC, LAMMPSTRJ, TNG, TRJ, and XYZ: supported for reading, but the reference does not list writing support for these trajectory formats.
That last distinction can save time when choosing an export format. If you need to pass results to another tool, check the Write column rather than assuming that a readable input format can also be generated from SAMSON.
Check whether the trajectory needs a companion file
Some workflows use a separate topology or structure file alongside the trajectory. The documentation specifically notes that AMBER NetCDF trajectories are loaded with an AMBER topology file, typically PARM7 or PRMTOP. SAMSON lists these topology extensions as readable molecular-structure formats, with their role described as being used when loading AMBER NetCDF trajectories.
So, if an NC, NCDF, or NCTRAJ file is involved, keep its matching topology file available and identify both when preparing the workflow. A trajectory file contains changing coordinates; the associated topology provides the structural information needed for that AMBER workflow. This is a practical first check before concluding that a trajectory is damaged or unsupported.
Use a simple troubleshooting sequence
- Identify the format. Check the extension and confirm whether the file is a structure or a trajectory.
- Confirm the direction. Look up whether SAMSON supports reading, writing, or both for that format.
- Gather related files. For AMBER NetCDF trajectories, include the corresponding PARM7 or PRMTOP topology file.
- Check extension-dependent formats. Some supported formats rely on SAMSON Extensions. The reference identifies PDBQT support with AutoDock Vina Extended and GROMACS project-file generation with GROMACS Wizard.
- Keep the original files unchanged. When testing a conversion or import, work from copies so you can return to the source data if the result is not what you expect.
SAMSON uses the chemfiles library to read and write some trajectory formats. If a format is not covered by the built-in options, SAMSON Extensions may offer additional support; the documentation also explains how to develop importers and exporters.
For the complete format list and notes on extension requirements, see the SAMSON supported-formats documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.