One of the most frustrating issues for molecular modelers using GROMACS is running an NPT equilibration—only to find that the system’s density is still oscillating or far from expected. If you’re spending time wondering whether you need to restart, modify parameters, or wait longer, you’re not alone. Fortunately, the GROMACS Wizard in SAMSON provides structured support to help you diagnose and resolve these situations in a few clicks.
When should you be concerned about the density?
After the initial energy minimization and NVT equilibration steps, NPT equilibration is responsible for stabilizing system density under constant pressure and temperature. But pressure is noisy. It fluctuates—sometimes dramatically. This makes density a more reliable indicator of equilibrium. If your simulation doesn’t show the density reaching a plateau, it’s a signal that more equilibration is needed.
Use the plots to monitor density
After running the NPT equilibration in SAMSON, the GROMACS Wizard generates plots tracking the evolution of pressure and density over time. These plots are crucial tools to check whether your system has achieved a stable state.
In this example, the density settles at around 1030 kg/m³, which is reasonably close to experimental values. But if your plot shows large swings or no steady plateau, you likely need to re-run NPT equilibration with more steps.
How to continue equilibration with prior results
If the system isn’t stable yet, rerun the NPT step using the output of the previous equilibration as input. The auto-fill button (
) makes this seamless:
- Click the auto-fill button next to the input file path.
- Verify the GRO file path points to your latest equilibration results (folder ending in
_npt). - Launch a second or third equilibration using the same or adjusted parameters.
Best practices for parameter settings
You can use the default GROMACS parameters for NPT equilibration to get started—typically 100 ps of simulation time. However, if you’re not reaching a stable density, increase the number of steps or consider tweaking:
- Barostat type: Use c-rescale for smoother convergence.
- Time constant: Recommended ≈ 5 ps.
- Temperature coupling: Match the NVT step settings to avoid temperature mismatches.
Don’t forget to check the final results
Once the run is done, SAMSON allows you to import the results and review the trajectory. You can analyze whether the density remains stable across the production frame or fluctuates, helping you decide on the next action.
If you’re uncertain whether to continue or stop, always ask: has the density plateaued? If not, iterate once more. And thanks to SAMSON’s automation, re-equilibrating is fast and painless.
To dig deeper into how to set up and interpret NPT Equilibration with the GROMACS Wizard, check out the full documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.