One of the most common frustrations for molecular modelers after completing energy minimization is realizing that the simulation system is not yet stable enough for meaningful dynamics. Structures might fly apart, unphysical fluctuations could persist, or temperatures deviate wildly. This usually points to skipping a critical step: NVT Equilibration.
In this post, we’ll explore how the GROMACS Wizard in SAMSON helps streamline this essential step through a guided and interactive interface. The goal is to get your system up to a stable, defined temperature before moving on to density optimization with the NPT ensemble.
Why NVT Equilibration Matters
After energy minimization reduces severe atomic overlaps or high-energy clashes, the system is still not in thermal equilibrium. Conducting dynamics right after minimization without controlling the temperature is risky, as the system hasn’t adjusted its internal velocities to match your desired thermodynamic conditions.
NVT Equilibration solves this by running a short simulation at constant Number of particles (N), Volume (V), and Temperature (T). This allows heat to flow appropriately and the system to gently “settle” into the simulation temperature.
Setting Up NVT Equilibration in SAMSON
In the GROMACS Wizard’s Equilibrate (NVT) tab, you start by providing input—ideally the minimized structure from the previous step. With an auto-fill button, you can instantly reuse the last output. Alternatively, you can manually select a GRO file or batch project.
Customizing Key Parameters
The Parameters section offers intuitive access to critical settings like the integration time step, number of steps, and temperature coupling. These can be retained as defaults for common setups or adjusted to suit specific system needs.
Temperature coupling can also be fine-tuned. For instance, protein and solvent might be coupled separately using velocity rescaling with stochastic terms (v-rescale). Click the + to add index groups, or go deep into the All… settings menu for advanced control.
Running and Monitoring the Simulation
Once configured, you can launch the equilibration locally, generate inputs, or send the job to the cloud. During runtime, the status is available under the Local jobs list for easy tracking.
Reviewing and Importing Results
After completion, you’re prompted to import results: the last frame, selected frames, or the full trajectory. You can also decide how to center the system and handle periodic boundary conditions. This flexibility lets you evaluate just what you need.
Analyzing Temperature Stability
To confirm that equilibration has succeeded, you can consult the temperature plot in the Plots section. A consistent plateau—like the one around 300 K in this example—indicates readiness for the next simulation stage.
Re-Running If Needed
If the desired temperature isn’t attained or stable, you can easily re-run the step by reusing the previous NVT outputs. Again, the auto-fill button comes in handy here.
In summary, proper NVT equilibration is more than a checkbox—it’s a vital transition that preps your system for reliable, reproducible simulations. Taking a few extra minutes here avoids much bigger headaches down the road.
Learn more in the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.