A molecular system can finish energy minimization and still need time before it is ready for the next stage of a molecular dynamics workflow. A common source of uncertainty is temperature: should you continue to NPT as soon as the simulation starts, or wait until the system settles? NVT equilibration gives you a focused way to bring the system toward its target temperature while keeping the number of particles and volume constant.
The practical challenge is not simply launching a run. It is deciding whether the temperature behavior is stable enough to proceed—and knowing what to do if it is not.
What NVT is doing in this workflow
NVT means constant number of particles, volume, and temperature. After minimization, this phase is used to stabilize the temperature. It is commonly followed by NPT equilibration, which is used to stabilize density. Treat the steps as a sequence: first inspect the temperature behavior, then decide whether to continue to NPT.
Start from the minimized system
Before launching NVT, make sure the energy-minimization step is complete and its output does not show unresolved problems. In GROMACS Wizard, the input can be a GRO file from minimization or a batch project from a previous step. If you are continuing from the previous successful run, the auto-fill control can populate the input path for you; otherwise, choose the GRO file directly.
This input choice matters when you need more equilibration. If the first NVT run has not settled, use the results from that run as the input to another NVT run. That continues from the current state rather than sending you back to the minimized structure.
Choose parameters with the goal in mind
The Parameters section contains commonly adjusted settings, including the integration time step and number of steps. Default values are intended for typical runs, but the appropriate duration depends on the size and contents of the system. The documentation notes that 50–100 ps is often sufficient; it is a useful starting point, not a guarantee that every system will be ready in that time.
In the advanced temperature-coupling settings, you can configure the thermostat, coupled groups, time constant, and reference temperature. For many projects, the tutorial suggests velocity rescaling with a stochastic term (v-rescale) and a time constant of about 1 ps. Also check that the temperature used for velocity generation corresponds to the coupling temperature. If you use multiple coupling groups, the number of time constants and reference temperatures should match the number of groups.
Position-restraint options are filled automatically based on the input system. If you have changed advanced settings and want to return to the tutorial’s baseline, use Reset. You can also load parameters from an MDP file or save the current parameters to one.
Read the temperature plot before moving on
After the job finishes, inspect the temperature plot in the Plots section. The goal is for the running average to reach a plateau around the target temperature. Small fluctuations are normal; the important question is whether the overall behavior looks stable enough to continue. In the tutorial example, the temperature stabilizes around the default target of 300 K.
If the system has not reached the target or the temperature has not stabilized, run additional NVT equilibration from the current NVT results and check again. Avoid treating the suggested duration as a pass/fail rule: use the observed temperature behavior to make the decision.
Run and review the job
You can generate project inputs, run locally, or launch a cloud computation. For a local run, progress is available in the Output window, and the Local jobs button lets you check job status. When results are ready, you can import the full trajectory, the last frame, or a selected frame range. Results are also saved in the specified results folder; NVT result folders have the suffix _nvt. If you cancel the import dialog, the results are not deleted and the plot can still be generated.
Once the temperature is stable enough for your workflow, continue to NPT equilibration. For the full procedure and interface details, learn more in the NVT equilibration documentation.
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