Molecular modeling and simulation often involve handling large trajectory files produced by molecular dynamics engines like GROMACS, AMBER, NAMD, LAMMPS, and Tinker. However, switching between simulation and visualization tools can feel like constantly battling with incompatible data formats and slow conversion steps.
SAMSON, the integrative platform for molecular design, provides built-in support for many common molecular dynamics trajectory formats, making the process much smoother when analyzing simulation results.
What are trajectory files used for?
Trajectory files record the atomic movements during a molecular dynamics simulation. They enable the analysis of structural evolution, energy changes, conformational transitions, and more. Loading these trajectories efficiently and without data loss is essential for in-depth analysis and clear visualization.
Trajectory formats supported by SAMSON
SAMSON simplifies opening and exporting trajectories thanks to its integration with the chemfiles library. Here’s a quick overview of the formats you can read and/or write directly within SAMSON:
- ARC: Tinker format
- DCD: Used by NAMD, CHARMM, and LAMMPS (read/write)
- LAMMPSTRJ: ASCII-based trajectory from LAMMPS (read only)
- NC: AMBER NetCDF format (read/write)
- PDB: Standard Protein Data Bank format (read/write)
- TNG: Next-generation GROMACS format (read only)
- TRR: GROMACS trajectory format (read/write)
- TRJ: Legacy GROMACS output (read only)
- XTC: Compressed GROMACS trajectory (read/write)
- XYZ: Simple coordinate format (read only)
Support for these formats allows users to open and analyze trajectories directly in SAMSON without intermediate conversion steps, helping focus on science rather than file handling.
Real benefits for molecular modelers
This level of format compatibility is especially useful in academic or multi-code projects. For example, you might run simulations in GROMACS, convert to NetCDF for post-processing with AMBER tools, and visualize the motion in SAMSON—all without leaving your workflow or writing custom scripts for format conversion.
Also, SAMSON handles topology dependencies such as PRMTOP for AMBER or PSF for CHARMM/NAMD when required, ensuring trajectory visualization is chemically accurate.
Just load and analyze
No extra configuration is needed. You simply import files the usual way, and SAMSON recognizes the appropriate trajectory reader. To save processed data (e.g., reduced-length trajectories, filtered by atom selection), SAMSON can export in formats like DCD, TRR, XTC, or NC, depending on your preferred analysis tool downstream.
What SAMSON doesn’t do (yet)
While it supports many formats for reading, SAMSON does not currently write TNG, TRJ, or LAMMPSTRJ files. Still, the core set of editable formats covers most workflows in molecular modeling projects.
To explore the full list of supported formats in SAMSON, refer to the official documentation: Supported Formats in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.