One common challenge molecular modelers encounter is knowing exactly when a system is truly ready for simulation after running equilibration steps. After all, launching a full-blown molecular dynamics (MD) simulation on an unstable system can mean wasted hours—or even days—of computational work.
This blog post focuses on a practical but often overlooked aspect of molecular modeling: how to confirm that your system is stable after the NPT equilibration phase before proceeding to simulation.
Why this matters
In molecular dynamics, the NPT ensemble equilibration (constant Number of particles, Pressure, and Temperature) helps stabilize the system’s density. But how do you know if it actually worked?
In SAMSON’s GROMACS Wizard, after running the NPT equilibration, the platform provides a convenient way to interpret results and see if your system is ready. If you’re unsure whether to proceed to production simulation—or perhaps rerun NPT—this feature could save you time and effort.
Step-by-step: Checking your system’s readiness
Once your NPT equilibration run finishes, SAMSON makes several tools available to help evaluate the results. Here’s how you can inspect what’s important:
1. Import the results
If you’ve run a single project, a pop-up will prompt you to choose how to import the results. Even if you launched a batch job, you can review its status in the Local jobs section.
The interface allows you to decide:
- How much of the trajectory to import (e.g., last frame only)
- What type of periodic boundary condition (PBC) treatment to apply
- How to center the system (e.g., on the protein)
2. Review density and pressure plots
Plots of system density and pressure vs. simulation time are auto-generated at the bottom of the GROMACS Wizard tab. These plots help assess whether your system reached a steady state.
A stabilized density (plateau) is a key indicator that NPT equilibration was successful. For example, if you see density hovering stably around ~1000 kg/m³ (depending on water model and system composition), then you’re likely good to go.
3. What if things aren’t stable?
If your plots show large fluctuations or the system’s density is still drifting, better to be safe than sorry. You can rerun the NPT Equilibration step from the latest results. Simply use the auto-fill button to load the last GRO file and try again under slightly adjusted parameters (e.g., longer equilibration time).
Bottom line
Taking a few moments to verify pressure and density stabilization after NPT equilibration can help ensure your simulations begin on a solid foundation. SAMSON’s built-in visual tools make this part of the workflow efficient and accessible.
Skipping this step is tempting—but can lead to unreliable simulation data. Better to double-check now than rerun everything later.
Want more detail on any of these features? Explore the full documentation here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.