Follow a suitable tutorial through preparation, minimization, equilibration, and production before adapting the system. Check force-field compatibility and monitor stability indicators rather than proceeding solely because a command completed. Preserve topology, parameters, and analysis scripts, and evaluate whether the sampled timescale is sufficient for the scientific question being asked.
This is best suited to researchers studying biomolecular dynamics. Before committing a larger project, account for these trade-offs: scientific setup requires expertise; compute requirements grow with system and timescale.
