A molecular dynamics run can finish successfully and still leave you wondering whether the system is ready for the next step. During NVT equilibration, the key question is not whether the temperature trace is perfectly flat—it is whether the system’s temperature is approaching and fluctuating around the intended target in a stable way.
This is a common point of uncertainty for molecular modelers. Moving on too soon can make it harder to judge later equilibration, while repeatedly changing settings without a clear reason can complicate the workflow. Here is a practical way to check the setup, interpret the plot, and decide what to do next using GROMACS Wizard.
Start with the right structure
NVT equilibration follows energy minimization. Before launching it, confirm that the minimized system looks reasonable and that the minimization output has no unresolved problems. The NVT input can be the resulting .gro file or a batch project produced by a previous step. If you are continuing the same workflow, the auto-fill button can populate the input path from the previous successful run; you can also select a GRO file yourself.
Keep the goal in view
NVT means constant number of particles, volume, and temperature. In this phase, the aim is to stabilize the temperature before proceeding to NPT equilibration, which is used to stabilize density. GROMACS Wizard provides typical default parameters, while the commonly adjusted settings—including the integration time step and number of steps—are available in the Parameters section.
A typical NVT run may take around 50–100 ps, but the system’s size and contents affect how long it takes. Treat that range as a starting point, not a guarantee. The useful check is the temperature behavior: its running average should reach a plateau around the desired value. Small fluctuations are normal; a perfectly level line is not the success criterion.
Check temperature coupling for consistency
In the advanced parameters, the temperature-coupling settings include the thermostat, coupled groups, time constant, and reference temperature. The tutorial gives velocity rescaling with a stochastic term (v-rescale) and a time constant of about 1 ps as a common choice for many projects. It also highlights an easy-to-miss consistency check: 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. The available groups depend on the system. Position-restraint options (POSRES*) are filled automatically based on the input system. For this tutorial, the instruction is to reset the parameters to their defaults; custom settings should be used deliberately for the needs of your project.
Use the plot to make the next decision
After launching Equilibrate locally, follow progress in the Output window or use Local jobs to check job status. Once the job finishes and the results are loaded, inspect the temperature plot in the NVT tab. The example below shows the temperature stabilizing around 300 K, the default reference value in the advanced parameters.
If the temperature has not reached the intended value or its running behavior is not stable enough to continue, you can run another NVT equilibration using the current NVT results as input. This makes the decision actionable: rather than treating the first run’s duration as a pass/fail rule, check the output and continue from the latest result when needed.
When importing results, you can choose the whole trajectory, the last frame, or a range of frames, as well as periodic-boundary-condition treatment and centering options. If you cancel the import, the results are not deleted, and the plot is still generated. Results are also available in the results folder; NVT output folders use the suffix _nvt.
Once the temperature is stable enough for your workflow, continue to NPT equilibration to stabilize density. For the complete walkthrough and interface details, learn more in the NVT Equilibration documentation.
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