Equilibrating a molecular system under pressure can be one of the more opaque steps for many modelers. After spending time preparing your simulation and stabilizing the temperature under the NVT ensemble, you’re faced with the task of ensuring your system reaches the appropriate density. This is where NPT Equilibration comes in—a critical step that often causes confusion or is overlooked.
NPT—short for constant Number of particles, Pressure, and Temperature—is essential when you’re preparing systems for simulation with tools like GROMACS. The idea is to slowly adjust the pressure, and monitor whether your molecular system reaches a realistic, stable density. In the SAMSON platform, the GROMACS Wizard simplifies this process with a tab tailored just for this task.
Start Seamlessly: Smart Input Detection
Choosing the correct input is the first hurdle. GROMACS Wizard offers a practical way to carry results from previous steps straight into the NPT phase. Thanks to the auto-fill button, you don’t need to track file paths manually—it intelligently detects outputs from steps like NVT Equilibration.
Adapting Parameters with Confidence
Once the structure is selected, you can modify simulation parameters like integration time step, number of steps, barostat type, and pressure reference. Don’t worry—defaults are pre-filled and often sufficient to get started, but tweaking is just a click away. Advanced options can be revealed via the All… button in case you need custom pressure coupling configurations, such as time constants or barostat methods.
Local? Cloud? You Decide.
When it’s time to run the equilibration, the Wizard gives you multiple options: run locally, send the job to the cloud (helpful for larger systems), or simply generate inputs to execute later. If resources are a concern or you’re working across multiple simulations, having these choices is a real productivity boost.
Visualizing Convergence
After equilibration, the GROMACS Wizard can import and process results. You’re not limited to dumping out a final structure—you can import the full trajectory, examine specific frames, and apply visualization settings such as Periodic Boundary Conditions and centering.
One of the most insightful parts is the Plots section. It automatically generates plots of pressure and density progression over time, allowing you to visually verify if the system has stabilized.
What to Watch Out For
Despite best practices, density might still drift or fluctuate if equilibration time is too short. If the plot shows instability or unmatched target values, simply re-run NPT Equilibration using the previous result files. Clicking the auto-fill button again helps you reuse the latest outputs quickly.
From Equilibrated System to Productive Runs
Only once pressure and density stabilize should you proceed to the main production simulation. Missteps here often propagate errors or artifacts, so it’s worth taking the time to do this right—and the GROMACS Wizard helps ensure that.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.