Temperature equilibration is a critical step in molecular simulations, especially when preparing systems to reflect physiological or experimental conditions. But if you’ve ever finished an NVT equilibration and noticed your system’s temperature still hasn’t stabilized at the target value—say, 300 K—you’re not alone. Many molecular modelers face this problem, and understanding both the causes and the solutions can save hours of reruns and recalibrations.
What’s supposed to happen?
During NVT equilibration (constant Number of particles, Volume, and Temperature), we aim to bring the system to the desired temperature using a thermostat. In GROMACS Wizard within SAMSON, the default setup uses velocity rescaling with a stochastic term (known as v-rescale), which is a good choice for most systems due to its balance between efficiency and stability.
So why does it sometimes fail?
Here are some common pitfalls that prevent successful temperature equilibration:
- Too short a simulation time: 50–100 ps is often cited as a guideline, but this depends on system size and composition. Larger or more complex systems may need more time to reach and stabilize at the target temperature.
- Inconsistent velocity generation settings: If the initial velocity generation temperature doesn’t match the thermostat’s reference temperature, the system can take longer to stabilize—or worse, fail to reach the desired temperature altogether.
- Poorly chosen coupling groups: By default, SAMSON couples the entire “System” group. But for heterogeneous systems (e.g., protein in water), splitting the system into meaningful coupling groups (like “Protein” and “non-Protein”) can give more realistic thermalization.
What can you do?
Here’s how to improve your NVT equilibration outcome using SAMSON’s GROMACS Wizard:
- Match your velocity generation temperature to the target coupling temperature. You’ll find this in the “Velocity generation” section of the wizard.
- Specify appropriate coupling groups: Click the + button next to the temperature coupling groups and select relevant components. Doing so allows finer control over how temperature is regulated per part of the system.
- Extend the simulation length if needed. If temperature hasn’t plateaued, just re-run the NVT equilibration using the output GRO file from the previous run by auto-filling it in the input field.
The temperature plot at the bottom of the NVT tab is also a handy diagnostic tool. If the curve shows large fluctuations and no plateau, it’s a good sign that more equilibration is needed.
Final thoughts
Temperature equilibration issues can be frustrating, but they’re not insurmountable. With the tools provided by SAMSON’s GROMACS Wizard—especially the rich control over thermal coupling strategies—you can iteratively fine-tune your setup for successful equilibration.
To learn more and explore each parameter in context, visit the original documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.