If you run molecular dynamics simulations, you already know that properly equilibrating your system is critical—but easy to overlook or shortcut. A common frustration among molecular modelers is seeing their simulations fail or provide unusable data because NVT equilibration was insufficient or improperly set up. Worse yet, re-running everything can cost hours of compute time, especially if your system is large.
In this post, we’ll look at why monitoring temperature stabilization is essential during the NVT equilibration step (constant Number, Volume, and Temperature), and how SAMSON’s GROMACS Wizard helps you avoid common mistakes efficiently.
Why Temperature Equilibration Matters
Temperature control in simulations is not just about setting a number. The simulation must reach a thermal equilibrium corresponding to this temperature. If it doesn’t, results from subsequent steps—like NPT equilibration or full production MD—will be unreliable, especially for properties that depend on energy distributions or conformational dynamics.
This is where users sometimes get caught: even if the simulation formally runs and ends, if the temperature fluctuates too widely or never stabilizes, those trajectories can lead to wrong interpretations.
How to Monitor Stabilization
After launching an NVT equilibration job (whether locally, on a cluster, or in the Cloud), SAMSON’s GROMACS Wizard automatically generates a temperature plot that lets you quickly assess the evolution of the system’s temperature over simulation time.
As a general rule:
- A successful NVT equilibration should show a temperature that stabilizes around your target value (e.g., 300 K).
- Some fluctuation is expected, but a trend line that oscillates significantly up or down indicates insufficient equilibration time.
This plot, available at the end of each NVT job, helps you decide whether to:
- Proceed to NPT equilibration, if stabilization occurred
- Or re-run NVT equilibration, starting from current results, if the temperature has not stabilized
What If the Temperature Didn’t Stabilize?
In SAMSON, it’s simple to start an additional NVT run:
- Click the auto-fill button to set the input to the latest results (
). - Repeat the equilibration with a longer time window, or adjust temperature coupling parameters if needed.
Tips for Efficient NVT Equilibration
- Start with 50–100 ps runs, then assess the temperature plot.
- Avoid guessing: use objective feedback from plots to guide equilibration length.
- You can save time with SAMSON’s local job manager—continue your workflow while the job runs.
- The generated results (e.g. plots, GRO, MDP files) are reusable across projects—no need to start from scratch.
More advanced users can fine-tune coupling groups, thermostats, and restraints in the Advanced Parameters section. But for most users, just checking the plot and re-running if needed prevents the most common issues.
Bottom line: be kind to your future self—take a moment to check that temperature really stabilized. SAMSON makes it quick, and it may save you hours later.
Learn more in 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 get SAMSON at https://www.samson-connect.net.