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SOMD Documentation

CLI References

Brife references to SOMD's command line interface (CLI).

TOML Input References

This is the references to SOMD's TOML input file. If you only use the somd command line interface, going through this documentation would be sufficient for you.

Python Interface References

This is not a set of standard API documentation, but may help the users figure out how to use SOMD as a library properly. This section is still a work in progress.

  1. SOMD basics.
  2. Set up the simulated system.
  3. Add atom groups to your system.
  4. Add constraints to your system.
  5. Set up potentials.
  6. Choose an integrator.
  7. Set up barostats.
  8. Set up trajectory writers.
  9. Set up system data loggers.
  10. Run a simulation.
  11. Evaluate one trajectory with other potentials.