A molecular dynamics run can finish without answering the question you care about: is the system ready for the next step? During NVT equilibration, the key check is whether the temperature is fluctuating around its target and behaving stably enough to continue. A noisy plot is not automatically a problem—small fluctuations are normal—but moving on before the temperature has settled can leave you unsure whether the system is properly prepared.
NVT keeps the number of particles, volume, and temperature constant. In the GROMACS Wizard workflow, it follows energy minimization and prepares the system for NPT equilibration, where density is stabilized. Treat NVT as a checkpoint, not merely a button to click: inspect the temperature behavior, decide whether it is stable enough for your workflow, and continue or run more equilibration accordingly.
Start with the right input
Use the GRO file produced by minimization or by a previous equilibration run, or select a suitable batch project. If you are continuing from the previous wizard step, the auto-fill button can populate the input path from the preceding successful run. This helps avoid accidentally starting from an unrelated structure.
Before launching, check that the minimized structure looks reasonable and that the minimization output has no unresolved problems. The wizard’s Load button can also be used before editing index groups or reviewing settings.
Keep the temperature settings consistent
The NVT tab provides commonly adjusted parameters, including the time step and number of steps. Other molecular dynamics settings are available through All…. Defaults are provided for typical runs, but settings may need to suit the particular system and project.
Pay particular attention to the relationship between temperature coupling and velocity generation: the documentation notes that the velocity-generation temperature should correspond to the coupling temperature. For many projects, the suggested starting setup is velocity rescaling with a stochastic term (v-rescale) and a time constant of about 1 ps. These are starting points, not a substitute for checking that the parameters fit your simulation.
If coupling multiple groups—for example, Protein and non-Protein—make sure the number of time constants and reference temperatures matches the number of groups. Position-restraint options are filled automatically based on the input system. If you are experimenting with settings, the advanced-parameter window lets you reset to defaults, load parameters from an MDP file, or save them to one.
Use the plot as a decision point
The required time depends on the size and contents of the system. The tutorial notes that 50–100 ps is often sufficient, but the more useful endpoint is the behavior of the running average: it should reach a plateau near the desired temperature. If it has not reached the target or has not stabilized, allow more time rather than treating a preset duration as proof of equilibration.
After the run, inspect the temperature plot in the Plots section. The example shown reaches approximately 300 K, the default reference temperature in the advanced parameters. Small fluctuations around the target are expected. If the temperature is still settling, launch another NVT step using the results of the previous NVT run as input.
You can run the job locally, generate inputs for another environment, or launch it in the cloud. During a local run, progress is available in the Output window and the Local jobs list. When results are ready, choose whether to import the full trajectory, the last frame, or a frame range. Canceling the import does not delete the results; the temperature plot is still generated.
Move on only when the trend is useful
NVT’s purpose here is to stabilize temperature, not density. Once the temperature behavior is stable enough for your workflow, proceed to NPT equilibration to work toward the desired density. If you need to revisit the full procedure, see the GROMACS Wizard NVT Equilibration tutorial.
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