One of the most common frustrations that molecular modelers encounter is when a simulation runs, but the system behaves erratically—either heating up quickly or displaying unstable behavior. A major reason? Skipping or misconfiguring the NVT equilibration phase.
In molecular dynamics, energy minimization is only the first step to prepare a system. Once your molecules are at a local energy minimum, they must be brought gently to your desired simulation temperature. This is where NVT equilibration comes in: a stage where the Number of particles (N), Volume (V), and Temperature (T) are kept constant, stabilizing your system before further steps such as NPT equilibration or full molecular dynamics.
Why does NVT equilibration matter? Because molecular systems are sensitive. Imagine placing molecules in a vacuum chamber without controlling the temperature—they would behave unpredictably. The NVT stage gently heats the system while keeping its volume fixed, ensuring energy is distributed gradually and fluctuations are reduced.
Using the GROMACS Wizard in SAMSON, this step becomes simple and visual. Start by switching to the Equilibrate (NVT) tab and selecting your input structure—either a .gro file from the prior minimization step or a previous project. If you’re continuing from a recent step, an Auto-fill button saves time by reusing output paths.
Once your structure is set, it’s time to configure simulation parameters. By default, SAMSON provides recommended values (often suitable for first runs), but you can modify them depending on your needs. There’s a balance to strike: too short a simulation might lead to unstable temperature; too long, and you waste resources. For most systems, 50 to 100 ps is a good starting point.
Clicking the All… button opens advanced parameters like thermostats and coupling groups. For example, by default, the velocity rescale thermostat (v-rescale) is used, which maintains the temperature smoothly with a time constant of about 1 ps. If your system has distinct parts (e.g., a protein in solvent), you can define custom temperature coupling groups such as Protein non-Protein.
Pro tip: You can even edit index groups directly from the interface—SAMSON lets you do this visually after loading your molecule.
With everything set, run your simulation locally or in the cloud. When it’s done, you can import your results and inspect plots of how the temperature evolved over time. A successful equilibration will show a temperature plateau at your target value, which is a good indication you’re ready to proceed to production simulations or NPT equilibration.
If you’re unsure whether the system has stabilized, just look at the temperature plot. Fluctuations are normal, but the trend should be stable. If not, you can easily relaunch another NVT equilibration using the previous results as input.
Learning how to equilibrate correctly is essential to producing reliable simulations and saving both time and compute credit. Thankfully, tools like SAMSON’s GROMACS Wizard automate the hard parts without hiding the important controls.
To learn more and follow the full walkthrough, visit the full GROMACS Wizard – NVT Equilibration documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.