A molecular dynamics system can finish energy minimization and still be far from thermal equilibrium. Starting the next stage too soon can leave you wondering whether the temperature is settling—or whether the simulation simply needs more time. NVT equilibration provides a focused way to bring the system toward its target temperature before moving on to density equilibration.
In an NVT ensemble, the number of particles, volume, and temperature are held constant. The immediate goal is not to make every temperature reading identical. Instead, look for the system’s running average to approach a plateau around the target value. Small fluctuations are normal; a temperature trace that has not yet stabilized is a reason to continue equilibration.
Start from a sensible input
Begin with the minimized structure and check that it looks reasonable and that the minimization output has no unresolved problems. In SAMSON’s GROMACS Wizard, open the Equilibrate (NVT) tab. You can provide the GRO file from minimization (or a previous equilibration run), or use a suitable batch project. If you are continuing from the previous step, the auto-fill button can populate the input path from the previous successful run.
Use the temperature plot as a decision aid
The default NVT parameters are intended for typical equilibration runs, and the commonly adjusted settings include the integration time step and number of steps. The duration depends on the system’s size and contents; the tutorial notes that 50–100 ps is typically sufficient, but this is a guide rather than a pass/fail rule. The useful question is whether the running average has reached a plateau at the desired temperature.
For example, the tutorial’s plot shows temperature stabilizing around the default target of 300 K. Use your own plot to assess the behavior of your system. If the temperature has not reached the target or is still settling, run another NVT equilibration using the results of the previous NVT step as input. This lets you extend the equilibration without treating a fixed duration as proof of stability.
Keep the target temperature consistent
In the advanced parameters, temperature coupling settings include the thermostat, coupling groups, time constant, and reference temperature. For many projects, the documented starting point is velocity-rescaling temperature coupling with a stochastic term (v-rescale) and a time constant of about 1 ps. The temperature used for velocity generation should correspond to the coupling temperature.
If you use multiple coupling groups—for example, Protein and non-Protein—make sure the number of time constants and reference temperatures matches the number of groups. For this tutorial, the recommended action is to reset the parameters to their defaults. Treat these values as setup choices to review for your system, not as a substitute for checking the resulting temperature plot.
Run, inspect, and continue when needed
GROMACS Wizard can generate inputs, run equilibration locally, or launch it in the cloud. After a local run, follow progress in the Output window or use Local jobs to check job status. When results are ready, you can import the trajectory, select frames, and choose periodic-boundary-condition treatment and centering options. If you cancel the import dialog, the results are not deleted, and the plot can still be generated.
Before moving on, check that the temperature is around the desired value and that its behavior looks stable enough for your workflow. If it has not settled, continue NVT from the current results. Once it has, proceed to NPT equilibration, where the next goal is to stabilize density. This simple checkpoint helps separate two different tasks: first temperature, then density.
For the complete walkthrough and parameter details, see the NVT Equilibration tutorial.
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