A molecular dynamics setup can be minimized and still be unready for production simulation. During minimization, the goal is to relieve unfavorable contacts; during NVT equilibration, the system is brought toward its target temperature while the number of particles and volume remain constant. A common point of uncertainty is deciding whether the temperature is stable enough to move on—or whether the system needs more equilibration.
The useful question is not whether every temperature value is identical. Small fluctuations are normal. Instead, look at the overall behavior: is the running average approaching a plateau near the target, and does the temperature plot look stable enough to continue?
Start from the right structure
NVT equilibration should follow a successful energy minimization. Before launching it, check that the minimized system looks reasonable and that the minimization output has no unresolved problems. In GROMACS Wizard, the input can be the GRO file from minimization or a suitable batch project. If you are continuing directly from the previous step, use the auto-fill button to select its output path; you can also choose a GRO file yourself.
This handoff matters: if the system has already undergone an NVT run but has not stabilized, use the results of that run as the input for the next one. That lets you extend equilibration from the current state rather than restarting from the earlier minimized structure.
Check the parameters that set the target
The NVT tab includes commonly adjusted parameters such as the integration time step and number of steps. The time required depends on the system’s size and contents; 50–100 ps is a typical starting range, not a guarantee that every system will be ready in that time. If the temperature has not reached or settled around its target, run additional NVT equilibration.
For temperature coupling, the documentation describes velocity rescaling with a stochastic term (v-rescale) and a time constant of about 1 ps as a common choice for many projects. Check that the temperature used for velocity generation corresponds to the coupling reference temperature. If you couple separate groups, such as Protein and non-Protein, make sure the time constants and reference temperatures match the number of groups. For a tutorial run, restore the default parameters before proceeding.
Use the plot as a checkpoint
After the run finishes, inspect the temperature plot in the NVT tab. In the tutorial example, the temperature stabilizes around 300 K, the default shown in the advanced parameters. Treat that as an example, not a universal target: the appropriate reference temperature depends on your project. Focus on the trend and the running behavior, rather than expecting a perfectly flat line.
If the system is still trending toward the target or has not settled enough for your workflow, continue with another NVT run using the current NVT results. Once the temperature is stable enough, the next stage is NPT equilibration, which is used to stabilize density. NVT is therefore a checkpoint in a workflow—not simply a fixed-duration box to tick.
Where to run and find results
GROMACS Wizard can generate input files for running elsewhere, launch a job locally, or submit a cloud computation. Local jobs can be monitored through the Local jobs button. When importing results, you can choose the trajectory frames and related import options; choosing not to import the trajectory does not delete the results, and the plot can still be generated. Results are also available in the specified results folder, with NVT runs identified by the _nvt suffix.
A concise decision rule: confirm a sound minimized input, verify that the coupling and reference temperature settings agree, inspect the temperature trend, and extend NVT from the latest results if it has not stabilized. For the full walkthrough, see the GROMACS Wizard NVT Equilibration documentation.
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