One common challenge in molecular dynamics is ensuring that your system reaches and maintains the desired temperature before you proceed with production simulations. If the temperature isn’t properly stabilized, results can be unreliable or misleading. This is where NVT equilibration becomes essential, and launching this step efficiently can save valuable time and computational resources.
The GROMACS Wizard Extension in SAMSON offers a streamlined interface for NVT equilibration. This post walks through a typical pain point—the setup and launch of NVT equilibration—and shows how SAMSON helps reduce the overhead in this crucial step.
Why NVT Equilibration Matters 🔬
Before diving into complex simulations, you need to ensure that your system reaches the set temperature and remains stable over time. NVT equilibration, which keeps the Number of particles, Volume, and Temperature constant, lets you achieve this. Within this ensemble, energy fluctuations caused by temperature transitions are minimized, resulting in a more reliable simulation environment.
Launching NVT Equilibration
Start by navigating to the NVT Equilibration tab in the GROMACS Wizard.
Input Structure Selection
Instead of manually selecting output files from previous steps, you can click the auto-fill button 
to pre-load the most recent GRO file or batch project. This saves time and avoids human error during manual file selection.
Parameter Configuration
Next, head to the Parameters section. While the defaults are generally appropriate, SAMSON offers the flexibility to modify key values like the time step and number of simulation steps to match your system needs.
You can even access advanced settings such as thermostat coupling methods and assign different temperature groups. For most simulations, using v-rescale with a time constant of ~1 ps works well.
When working with structured systems like proteins, it’s easy to define groups (e.g., protein / solvent) via the Edit index groups option.
Running the Equilibration
Click Equilibrate locally to run the process directly on your PC. Jobs run in the background, allowing you to continue working within SAMSON.
Your job statuses are easily accessibly via the Local jobs manager:
Checking the Output 📈
After the run, you can import simulation results using a variety of options—choose the last frame, full trajectory, or customize periodic boundary conditions.
Visualizing the Results
One of the most helpful tools is the plot of temperature vs time, which appears at the bottom of the NVT tab. This lets you clearly assess whether equilibration was successful.
Ideally, your plot should show the system’s temperature stabilizing around your target value (e.g., 300 K). If not, it’s easy to re-run the step using results from the previous attempt. Just use the auto-fill button again to load the latest output.
Wrap-Up
For molecular modelers, getting stuck configuring or validating temperature equilibration can be an unnecessary time sink. SAMSON’s GROMACS Wizard simplifies this step—intelligently filling input paths, providing adjustable presets, and presenting clear visual reports—all with a few clicks.
To explore the full guide for NVT Equilibration in the GROMACS Wizard, click here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.