One of the most common hurdles when setting up molecular dynamics (MD) simulations is achieving a stable temperature before collecting meaningful data. If you’ve ever encountered temperature drifts or fluctuations in your system, chances are the equilibration phase wasn’t properly handled.
In GROMACS-based simulations, temperature equilibration is typically carried out using the NVT ensemble—which maintains the Number of particles, Volume, and Temperature constant. This is an essential step after energy minimization, especially before pressure equilibration (NPT), to avoid non-physical artifacts in the data.
Let’s explore how the GROMACS Wizard in SAMSON helps streamline this often-overlooked step by handling input preparation, parameter tuning, job execution, and result verification—all from a single interface.
Why accurate NVT equilibration matters
Temperature fluctuations can affect not only energetic profiles but also trajectory convergence in MD. With poorly stabilized systems, you might encounter simulation crashes or biologically unreliable behavior. The goal of the NVT step is to bring the system to your target simulation temperature (say, 300K) and let it settle.
Auto-filling smart inputs
Need to equilibrate a structure that was just minimized? No need to go hunting for the path to that file manually. The NVT tab offers an auto-fill button that automatically loads your last minimized GRO file or project—a small but essential feature that reduces errors and speeds up your workflow.
Setting the right parameters
Equilibration timeframes vary, but generally, 50–100 ps is sufficient. SAMSON makes parameter setup intuitive: time steps, thermostat types, and position restraints are preloaded and visible in the Parameters section—which you can tweak or reset to defaults at any point.
Fine-tuning thermal coupling
Want more control? You can define which groups of atoms (e.g., protein vs solvent) are coupled to separate thermostats and how their temperatures evolve using the advanced settings.
Visualizing stabilization
After the run completes, you’re not left guessing. A plot showing the system’s temperature over time is automatically generated. If the temperature plateaus near your target (like 300K), you’re good to go. Otherwise, rerun the equilibration using the latest output automatically selected via auto-fill.
What if it didn’t stabilize?
If your system didn’t stabilize, simply repeat the NVT step with output from the previous run. This iterative behavior ensures convergence before you move on to NPT equilibration. With a couple of clicks, control and reproducibility are at your fingertips.
Learn more details and view the full documentation on NVT equilibration in SAMSON at this page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.