A simulation can finish successfully and still leave you with a frustrating question: which file should you open to see the molecules move? Molecular dynamics workflows often produce several files, and their extensions can be unfamiliar. Choosing the wrong one—or expecting a viewer to write a format it only reads—can interrupt an otherwise straightforward analysis.
SAMSON supports a range of molecular trajectory formats. The useful first step is to identify the file’s role and check whether SAMSON can read it, write it, or both. Here is a quick guide based on the supported-format list:
| Format | What it is | SAMSON support |
|---|---|---|
| ARC | Tinker trajectory format | Read |
| DCD | Binary trajectory used by CHARMM, NAMD, or LAMMPS | Read and write |
| LAMMPSTRJ | ASCII trajectory produced by LAMMPS’ dump command |
Read |
| NC | AMBER NetCDF trajectory; aliases include NCDF and NCTRAJ | Read and write |
| PDB | Standard PDB file; read aliases include ENT, VDB, PDB1, and PDB2 | Read and write |
| TNG | Trajectory Next Generation file | Read |
| TRR | GROMACS TRR trajectory | Read and write |
| TRJ | GROMACS TRJ trajectory format | Read |
| XTC | GROMACS compressed trajectory | Read and write |
| XYZ | Simple coordinate trajectory format | Read |
“Read” and “write” answer different questions. If a format is listed as readable, SAMSON can import it. If it is listed as writable, SAMSON can export data in that format. A blank cell in the documentation’s table means that capability is not listed there; it is a reason to check before planning a conversion, not a statement about what other software can do.
Pay attention to the simulation package and the exact extension. For example, the documentation identifies DCD as a binary trajectory associated with CHARMM, NAMD, or LAMMPS, while LAMMPSTRJ is the ASCII trajectory written by LAMMPS’ dump command. GROMACS has several entries: TRR and XTC are listed as readable and writable, while TNG and TRJ are listed as readable. Those distinctions can help you choose an output format that fits your next step.
Some trajectories are used with a separate topology file. The documentation specifically notes that an AMBER topology file—PARM7 or PRMTOP—is used when loading AMBER NetCDF trajectories. If you have an NC, NCDF, or NCTRAJ file, keep the corresponding topology available and check the workflow for loading molecules rather than treating the trajectory as a complete molecular system by itself.
One more detail: SAMSON uses the chemfiles library to read and write some trajectory formats. The format reference does not identify which individual entries use that library, so consult the format listing and your workflow rather than assuming every format behaves identically.
A practical pre-flight check: note the file extension, identify the simulation package that produced it, confirm that SAMSON lists the required read or write capability, and keep any associated topology file together with the trajectory. This small check can save time when moving simulation results between tools or preparing data for someone else.
For the complete list of supported formats and related import/export guidance, see the SAMSON supported formats reference.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at www.samson-connect.net.