One of the most delicate steps in molecular simulation workflows is the NPT (isothermal-isobaric) equilibration phase. After energy minimization and temperature stabilization via NVT equilibration, the next goal is to ensure that your system reaches a stable density under the desired pressure and temperature conditions. Missteps here can result in flawed results in your production simulations, especially when density shifts or fluctuations remain unchecked.
The GROMACS Wizard in SAMSON simplifies this step, but there are still important decisions modelers must make. Below, we outline a few key points to help you confidently configure and execute an NPT equilibration using the platform—while avoiding some tough-to-debug errors later on.
Start with the Right Input 📄
NPT equilibration depends on the prior state of your system. Before launching this step, ensure your system has been either:
- Minimized (from the Energy Minimization step), or
- Subject to NVT equilibration.
Use the auto-fill button 
to grab the latest valid input automatically. This small feature significantly reduces the chance of accidentally feeding in an incorrect or outdated GRO file.
Choose Parameters with Purpose ⚙️
The wizard provides default molecular dynamics parameters, but it’s still important to review them. Commonly adjusted parameters include:
- Integration timestep
- Number of simulation steps (e.g., 100 ps minimum for observing density evolution)
To access more advanced settings, click the All… button 
. Restoring defaults, loading settings from a prior project, or saving current parameters are just a click away.
Check Temperature and Pressure Coupling Carefully
For pressure coupling, the exponential relaxation method with a stochastic term (e.g., c-rescale) and a time constant of around 5 ps is commonly used:
Important: Ensure your temperature coupling settings match those in the NVT equilibration. Any mismatch can result in inconsistent thermodynamic behavior during your run—an often overlooked issue.
Launching and Monitoring the Equilibration 🚀
The GROMACS Wizard gives you options to run the NPT equilibration locally or in the cloud. For initial functional testing of your setup, we recommend running it locally using the Equilibrate locally button. Progress is visible through the Output window, and active jobs are managed via the Local jobs panel:
Has the System Stabilized? 📉
When your run is finished, you’ll get plots showing the time evolution of pressure and density. Assess whether the density has stabilized — ideally near its target value (e.g. 1000 kg/m3 for water):
If the density hasn’t flattened out, no worries: just re-run the NPT equilibration using the last output as input. Again, the auto-fill button makes this step easier.
Final Tips
- Check the results folder—it’s named using the launch timestamp and step type (e.g.
_npt). - If you want to reimport results later, you can choose to import the full trajectory or just selected frames.
NPT equilibration isn’t just another procedural step; it’s a checkpoint for system readiness before moving into production simulation. Paying attention here can spare you from confusing simulation artifacts down the road.
To learn more, visit the full tutorial page on NPT Equilibration using GROMACS Wizard.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.