When preparing molecular simulations with GROMACS, reaching the desired temperature during the NVT (constant Number of particles, Volume, and Temperature) equilibration phase can be trickier than expected. If your system doesn’t stabilize at the target temperature, everything downstream—like NPT equilibration or MD production runs—could be compromised. Fortunately, SAMSON’s GROMACS Wizard offers a GUI that simplifies this crucial step and makes temperature control more intuitive, even for less experienced users.
One common source of confusion lies in managing temperature coupling. That is, how your system adjusts to maintain a specific temperature during simulation. In GROMACS, this is handled through thermostats, and the SAMSON GROMACS Wizard allows you to configure these settings visually, without editing cumbersome MDP files directly.
In the NVT Equilibration tab, scroll down to find the Temperature coupling section:
Here, you can choose the thermostat method—by default, it uses v-rescale, a popular choice that introduces a stochastic term to preserve ensemble correctness. You can also set parameters like the time constant (typically around 1 ps) and the reference temperature (e.g., 300 K).
But what if your system is complex, like a solvated protein? In this case, coupling temperature globally may not be ideal. SAMSON GROMACS Wizard lets you specify distinct index groups for selective coupling. Simply click the + button to open a dialog and select groups such as Protein and non-Protein. This way, different parts of your system can reach thermal equilibrium at different rates—matching the physical reality better.
To create custom index groups, load your structure and click Edit index groups. This feature gives you control over how temperature is applied without requiring command-line editing or stopping to process your system externally. If things go wrong, you can always reset the parameters to the default System group:
Watch out for mismatches between the reference temperature in the Temperature coupling and the initial velocity generation temperature—SAMSON automatically aligns these values, but double-checking can’t hurt.
Monitoring the output is just as important. After running the NVT Equilibration, SAMSON automatically plots the temperature evolution over simulation time. A stable plateau indicates your system has reached thermal equilibrium:
If the desired temperature isn’t reached or still fluctuates significantly, simply use the results of this run as input for another round of NVT Equilibration. SAMSON’s auto-fill button makes this seamless.
Temperature coupling can often feel like fine-tuning a sensitive instrument. But with the visual, step-by-step approach in SAMSON GROMACS Wizard, what once felt like “molecular guesswork” becomes a transparent and controlled setup process.
To learn more, visit the full documentation page for GROMACS Wizard – NVT Equilibration.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from www.samson-connect.net.