A molecular dynamics run can be technically complete and still leave you wondering: has the system actually settled at the temperature I intended? That uncertainty matters. Move on too soon, and the next stage begins before temperature is stable; keep running without checking, and you may spend time on equilibration that is already sufficient.
NVT equilibration is the temperature-stabilization stage after energy minimization. The ensemble keeps the number of particles, volume, and temperature constant. The practical goal is not to make every instantaneous temperature reading identical. Small fluctuations are normal. Instead, check whether the running temperature behavior settles around the target and looks stable enough for your workflow.
Start with a trustworthy input
Before launching NVT, make sure minimization has completed and that the resulting system looks reasonable, with no unresolved problems in the minimization output. In the GROMACS Wizard, open the Equilibrate (NVT) tab and provide either the GRO file from minimization (or an earlier equilibration run) or an eligible batch project. If you are continuing directly from the previous step, the auto-fill button can populate the input path from the previous successful run.
Choose settings with the goal in mind
The Parameters section contains commonly adjusted settings, including the integration time step and number of steps. The appropriate run length depends on the system’s size and contents. As a general guide, the documentation notes that 50–100 ps is typically sufficient, but the temperature plot—not a fixed duration—should guide your decision. If the target has not been reached or the running behavior has not stabilized, continue with additional NVT equilibration using the current NVT results as input.
For many projects, the documented starting point for temperature coupling is velocity rescaling with a stochastic term (v-rescale) and a time constant of about 1 ps. Check that the temperature used for velocity generation corresponds to the coupling temperature. If you use multiple temperature-coupling groups, make sure the number of time constants and reference temperatures matches the number of groups. The position-restraint options are filled automatically based on the input system. For this tutorial, the recommended action is to reset parameters to their defaults.
Use the plot as a decision aid
After the job finishes, inspect the temperature plot in the Plots section. In the tutorial example, the temperature stabilizes around the default target of 300 K. Use the plot to ask two simple questions: Is the temperature around the intended value? Does its running behavior look stable enough to continue? A few small variations do not automatically mean the run has failed; the documentation explicitly notes that small fluctuations around the target are normal.
If the answer to either question is no, run NVT again from the latest equilibration results and review the plot afterward. If the temperature is stable enough for your workflow, proceed to NPT equilibration, where the next goal is to stabilize density. This gives you a practical checkpoint rather than treating a completed job as proof that equilibration is complete.
Keep the results useful
You can run the job locally, generate inputs for another environment, or launch it in the cloud. Once results are ready, choose whether to import the full trajectory, only the last frame, or a range of frames. The results folder is identified by its launch date and time and has the suffix _nvt. If you do not want to import the trajectory, cancelling the import does not delete the results, and the plot is still generated. You can also save the plot from the figure for later review.
The key habit is simple: verify the temperature behavior before moving on, and extend equilibration when the evidence says it is needed. For the full workflow and interface details, see the NVT Equilibration tutorial.
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