One of the most common challenges in molecular dynamics simulation is ensuring that a system reaches realistic density and pressure conditions before launching a production run. If you’ve ever struggled with fluctuating densities or simulation artifacts due to poorly equilibrated systems, NPT equilibration may be what your workflow needs.
In this blog post, we’ll walk through NPT equilibration using the GROMACS Wizard Extension in SAMSON — offering a practical approach to setting up and executing this crucial step.
Why NPT Equilibration?
After minimizing energy and stabilizing temperature (NVT ensemble), the system may still not reach the appropriate density. This is because in the absence of external pressure, molecules might not settle into a realistic volume. NPT equilibration — where the number of particles, pressure, and temperature are kept constant — is used to simulate more realistic conditions and ensure proper system compactness.
Getting Started: Input Files
To begin, switch to the Equilibrate (NPT) tab. You can provide input as a .gro file from the previous step (e.g., NVT Equilibration) or as a batch project. Not sure what to select? Use the auto-fill button 
to select the last valid output automatically.
Customizing Parameters (But Keep It Simple)
The GROMACS Wizard provides default parameters suitable for most scenarios, but it also allows for customization. For example, adjusting the number of steps or integration time step can help if your simulation isn’t stabilizing.
To go deeper into settings — like modifying barostat values or enabling position restraints — click the All… button to open advanced parameters. For most users, default pressure coupling settings using exponential relaxation (c-rescale) with a time constant around 5 ps work well.
Running the Simulation
You have three execution options:
- Generate inputs for external execution
- Equilibrate locally with your computer’s resources
- Equilibrate in the cloud, ideal for demanding systems
Click on Equilibrate locally if you’re running a small to medium-sized system and want quick feedback.
Review Your Results
Once the job is complete, GROMACS Wizard offers flexible import options: entire trajectory, select frames, center on specific atoms, and more. The results folder is automatically generated and well-organized by date and job type (e.g., _npt suffix).
Density and Pressure Plots
Stability checks are visual: GROMACS Wizard plots pressure and density evolution over time. Ideally, the density graph should plateau — a sign your system is ready for production runs. If not? Run NPT equilibration again with your last trajectory as input.
Conclusion
NPT equilibration is often underestimated but critical for the quality of simulations. The GROMACS Wizard in SAMSON simplifies what is typically a multi-step process into an intuitive workflow. Whether you are running simulations locally or in the cloud, this makes your journey from raw structure to simulation-ready system much smoother.
To learn more, visit the full documentation page: GROMACS Wizard – NPT Equilibration.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at www.samson-connect.net.