In molecular dynamics simulations, a well-managed NPT equilibration is only half the journey: importing the results correctly can be just as critical. Many researchers using GROMACS encounter confusion or inconsistencies at this stage—not because their simulation failed, but because pressure and density results were not examined or imported appropriately. If you’ve ever asked yourself whether to import full trajectories or single frames, which periodic boundary conditions to use, or how to verify stability, you’re not alone.
Thanks to the GROMACS Wizard in SAMSON, handling result import after NPT equilibration can be much smoother, especially if you know where to look.
Know What to Import (and Why)
When the NPT equilibration finishes, a pop-up gives you choices:
- Full trajectory: Ideal if you’re planning an analysis of the system’s behavior across time or preparing an animation.
- Last frame only: Useful when you’re preparing the system for a production run and care about the equilibrated structure more than the dynamics.
- Frame range: Enables you to focus only on the stable portion once the system has equilibrated.
Different projects demand different strategies. But misunderstanding these options may result in using frames that are not truly equilibrated—an easy mistake with consequences for long simulations.
Pay Attention to System Centering
When importing, you can choose how the system is centered. Centering your simulation on critical components, like the protein or the solvent box, impacts how the simulation looks and how easy it is to analyze. Total clarity in post-processing depends on smart centering decisions here.
Check System Density Before You Move On
Even if the run completed successfully, don’t skip reviewing the plots. These plots show how pressure and density evolved over time. Did the density reach a plateau? Was the pressure too noisy?
In one example, the density stabilized at 1030 kg/m³—close enough to the expected ~1008 kg/m³ for the SPC/E water model. A difference like this is acceptable, but a drifting density or a highly fluctuating pressure may indicate that more equilibration is needed.
If the density hasn’t stabilized yet, no worries—just launch another NPT equilibration, this time using the most recent result as the input. Thanks to the auto-fill option (
), setting that up only takes seconds.
Outputs Are Safe—Cancel Without Fear
If you’re unsure how to import or wish to delay it, you can click Cancel. SAMSON doesn’t delete your results. You can always return later and reload the data without loss. Results are stored in a folder clearly timestamped with a _npt suffix for easy retrieval.
Final Tips
- Always double-check that the imported structure corresponds to the end of the plateau phase in your plot.
- Save plots if you’re reporting or comparing trajectories. The Save button (
) is built right into the interface.
Don’t let simulation results go to waste because of small oversight in result import. With a few clicks and a careful look at the plots, you can be confident your system is ready for production simulations.
Learn more in the full GROMACS Wizard NPT Equilibration tutorial.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.