One of the persistent challenges in setting up molecular dynamics simulations is ensuring that a system reaches the correct density under realistic conditions. After temperature stabilization during NVT equilibration, many researchers hit a roadblock: how to efficiently transition their system to a physically accurate density before production MD begins. This is where NPT equilibration comes in—and SAMSON’s GROMACS Wizard makes this phase much easier to manage.
This post walks you through NPT equilibration using SAMSON, focusing on solving a common pain of molecular modelers: achieving stable system density before launching long simulations. The goal is to bring value to both new and experienced users by explaining the process in a clear, visualized way.
What Is NPT Equilibration?
NPT stands for constant Number of particles, Pressure, and Temperature—an ensemble used to bring the system’s pressure and density to equilibrium while maintaining a fixed temperature. This step is also referred to as isothermal-isobaric equilibration. It’s vital before moving forward with production simulations.
Starting NPT Equilibration in SAMSON
To begin, switch to the Equilibrate (NPT) tab in the GROMACS Wizard Extension. If you’re continuing from a previous equilibration step (e.g., NVT), simply use the auto-fill button 
to populate the input path automatically.
Choosing Parameters Wisely
While SAMSON provides sensible defaults, you can modify parameters in the Parameters and Advanced Parameters sections. Settings like integration time step, number of steps, and pressure coupling methods can be customized. For example, using c-rescale as the barostat with a time constant of 5 ps is a good starting point for many systems.
The POSRES (position restraint) options are set automatically. You can explore all mdrun parameters by clicking the All… button.
Running and Monitoring
To launch NPT equilibration, choose between these options:
- Generate inputs: For external cluster execution.
- Equilibrate locally: Run on your PC.
- Equilibrate in the cloud: Ideal for resource-intensive systems.
Monitoring progress is seamless with the built-in job manager. You can keep using SAMSON while your job runs. Once completed, import the results using the pop-up or check them via the Local Jobs tab.
Interpreting the Results
One advantage of the Wizard is immediate visual feedback. After the job completes, SAMSON generates density and pressure plots. These are key to confirming whether equilibration was successful.
In the example, the system stabilizes around 1030 kg/m³, very close to expected values for SPC/E water. Fluctuations are normal, but if the average doesn’t plateau, re-running NPT using the outputs of the previous step is recommended.
Troubleshooting: What If Density Isn’t Stable?
It’s not uncommon for equilibration to take longer than expected, especially in complex systems. If your density hasn’t stabilized:
- Ensure temperature and pressure coupling settings match those used previously.
- Increase the number of steps.
- Rerun the step with the latest .gro output using the auto-fill option.
Only once density converges should you proceed to the production run phase.
To learn more, visit the full documentation page here: NPT Equilibration in GROMACS Wizard.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.