One of the key challenges in molecular dynamics simulations is ensuring your system reaches and maintains a stable target temperature before production runs. For many molecular modelers, this step — known as NVT equilibration — can be a source of frustration, especially when temperature oscillations refuse to settle.
If you’ve faced unsteady temperatures or aren’t sure how to smoothly transition from energy minimization to proper thermal equilibration, the NVT Equilibration step in the GROMACS Wizard Extension for SAMSON could be a practical solution to make this process more transparent and repeatable.
Why NVT Equilibration Matters
NVT equilibration brings your simulation system to a target temperature before further steps, such as pressure equilibration (NPT) or production molecular dynamics simulations. Without this step, simulations may begin under unrealistic thermal conditions, potentially affecting the reliability of your results.
The canonical ensemble (NVT) keeps the Number of particles (N), Volume (V), and Temperature (T) constant. This setup is ideal for initial thermalization, allowing the system’s kinetic energy (hence temperature) to reach the specified reference value.
Using GROMACS Wizard in SAMSON to Run a Local NVT Equilibration
Let’s focus on the streamlined workflow for running NVT Equilibration locally using GROMACS Wizard in SAMSON:
1. Start with the Right Input
You can launch the NVT Equilibration using input from the energy minimization step — either a .gro file or a SAMSON batch project file:
Clicking the Auto-fill button saves time and avoids manual file browsing — it inserts the correct path from your previous successful run automatically.
2. Adjust or Accept Parameters
The default parameters are well-suited for general cases, but you can customize several options, including:
- Time step and number of steps
- Thermostat type (e.g., velocity-rescaling with noise)
- Reference temperature (e.g., 300K)
Parameters can also be saved or imported using MDP files for consistency across projects.
3. Launch and Monitor the Run
Click Equilibrate locally to start the process using your computer’s resources:
The job runs in the background so you can continue working. You’ll receive a pop-up once completed, offering to import results.
4. Review and Verify
You can inspect the temperature evolution during equilibration through an auto-generated plot:
An ideal outcome is a flat line around the target temperature. If stabilization hasn’t occurred, just repeat the NVT equilibration using the output of the current run as input.
Conclusion
The local NVT equilibration workflow in GROMACS Wizard for SAMSON offers a clear and visual approach to one of the most crucial — and frequently misunderstood — stages in molecular dynamics preparation. Whether you’re starting from a minimized system or iterating to reach a steady temperature, this integrated process removes much of the guesswork.
Learn more by visiting the full documentation here: https://documentation.samson-connect.net/tutorials/gromacs-wizard/nvt-equilibration/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here: https://www.samson-connect.net