Have you ever run a simulation where the pressure never quite stabilizes? Or where your system density keeps drifting, despite starting from an apparently well-prepared structure? If so, you’re not alone. One of the trickiest aspects of preparing a molecular dynamics simulation is ensuring the system has properly equilibrated—not just in terms of temperature, but also pressure and density.
This is where NPT equilibration comes in. In this blog post, we’ll explore how to prepare and run NPT equilibration using the GROMACS Wizard in SAMSON, a visual and intuitive environment for molecular modeling that simplifies demanding computational workflows.
What is NPT Equilibration and Why Is It Important?
NPT stands for constant Number of particles, Pressure, and Temperature—also known as the isothermal-isobaric ensemble. After energy minimization and NVT (constant volume and temperature) equilibration, running an NPT simulation allows the system’s volume to adjust so that the pressure matches the target (typically 1 atm), stabilizing the density in the process.
Skipping or misconfiguring this step may result in unphysical densities or unstable pressure profiles, causing artifacts in the subsequent production simulation. The GROMACS Wizard in SAMSON makes this critical step much easier. Let’s take a closer look.
Quick Setup in the GROMACS Wizard
To launch NPT equilibration:
- Switch to the Equilibrate (NPT) tab in the GROMACS Wizard.
- Load a structure minimized and temperature-equilibrated using NVT. You can do this manually, or just click the auto-fill button to load the previous result automatically.
- Adjust simulation parameters (or leave defaults for a quick start).
Fine-Tuning Parameters
While default values are a good starting point, you may wish to tweak simulation length, time-step, or pressure coupling parameters.
For example, a relaxation time constant of ~5 ps and the c-rescale barostat are commonly used defaults for exponential pressure relaxation:
If you’re unsure how long to run the equilibration, 100 ps is a reasonable initial value. You can always rerun with a longer time if things haven’t stabilized.
Running and Monitoring Your Job
GROMACS Wizard offers three execution modes: generate inputs, compute locally, or launch in the cloud. For small to medium systems, selecting Equilibrate locally is often the fastest way forward.
Thanks to SAMSON’s job manager, GROMACS jobs run in the background so you can continue preparing other simulations or analyzing data.
Evaluating the Results
Once the run completes, you can import the trajectory or just specific frames. But the most immediate visual clue is from the plots:
Here, you’re looking for the density to reach and level off around a reference value. Water, for instance, should stabilize close to 1000 kg/m³ (depending on the model used).
Still Not Stable?
It happens. If the density hasn’t stabilized yet, you can simply launch a second NPT run using the output from the first as input. SAMSON helps streamline this with the repeatable input auto-fill option.
If you’re consistently seeing erratic pressures or density drifts, check that your system isn’t too small or placed under unrealistic constraints. Also make sure the temperature and velocity settings match between NVT and NPT steps.
For a step-by-step walk-through, including advanced suggestions, visit the full documentation: GROMACS Wizard NPT Equilibration Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.