One of the common bottlenecks in molecular dynamics setup is hitting that sweet spot where the system’s density stabilizes. If you’ve minimized your structure, performed NVT equilibration, and you’re now at the pressure coupling stage but your results are bouncing unpredictably, this post is for you.
Let’s look at what happens during the NPT equilibration phase in SAMSON’s GROMACS Wizard and how you can interpret results and know when to rerun your simulations — saving valuable time and avoiding misinterpreted outcomes.
Why Does NPT Matter?
NPT equilibration helps your system reach the right density by simulating under constant Number of particles, Pressure, and Temperature (the NPT ensemble, also known as the isothermal-isobaric ensemble). The goal is to pressurize the system so that it reaches a realistic density, preparing it for subsequent production runs.
Density Still Fluctuating? Consider This
After running the NPT step, you may check the pressure and density plots and notice wide fluctuations or a trend that doesn’t plateau. Is it failing? Not necessarily — pressure is inherently noisy. However, the running average of the density should typically show signs of convergence.
If the density does not stabilize (e.g., continues rising or falling by a noticeable margin over time), you might need to:
- Increase the simulation duration (e.g., try 200 or 300 ps instead of 100 ps).
- Ensure your thermostat and barostat settings match your previous equilibration steps.
- Re-run NPT equilibration by feeding in the last frame from the previous NPT attempt.
How to Rerun the NPT Step Easily
GROMACS Wizard provides a handy auto-fill button (
) to load the input GRO file from your last successful equilibration step. If the density hasn’t settled, just rerun using that recent result to continue refining your system’s pressure behavior.
Visual Clues
The plots can help you tell if you’re done. In the example below, the density stabilizes at around 1030 kg/m3. That’s close to the experimental value for water (1000 kg/m3) and the expectations for common water models like SPC/E (~1008 kg/m3):
If your graph looks like this — a flattened curve toward the expected value — you’re good to proceed. If not, return to the NPT tab and try modifying your parameters or increasing simulation length.
Bonus Tip: Managing Local Jobs
You can track the status of your simulations with the Local jobs button. This feature lets you launch multiple jobs in sequence and keep an eye on what’s still running without blocking your SAMSON session.
Keeping an eye on your system’s density behavior can save you from erroneous runs and wasted computing resources. Whether you’re running locally or in the cloud via SAMSON, rerunning an NPT step is easy and can make a world of difference in simulation readiness.
To learn more, head over to the full documentation: NPT Equilibration Tutorial.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.