A temperature plot can look busy even when an NVT equilibration is progressing normally. That makes a common molecular-modeling decision surprisingly difficult: should you continue to NPT, or give the system more time? The useful signal is not whether every point sits exactly on the target temperature. It is whether the temperature’s running behavior has settled around that target well enough for your workflow.
NVT means constant number of particles, volume, and temperature. In this stage, the goal is to bring the system to the desired temperature in a controlled way. Density stabilization comes later, during NPT equilibration. Keeping those goals separate makes it easier to interpret what this step is—and is not—intended to accomplish.
Start from a sensible input
Run NVT after energy minimization, and first check that the minimized system looks reasonable and that the minimization output has no unresolved problems. GROMACS Wizard can take either the resulting GRO file or a batch project from the earlier step. If you are continuing a previous successful run, the auto-fill button can populate the input path; otherwise, select the GRO file yourself.
This small check prevents a frustrating detour: confirming that the job ran is not the same as confirming that it started from the structure you intended.
Read the plot for stability, not perfection
After the job finishes and results are loaded, inspect the temperature plot in the Plots section. In the tutorial example, the temperature stabilizes around 300 K, the default reference temperature shown in the advanced parameters. Small fluctuations around the target are normal. The practical question is whether the temperature has reached the desired range and its running behavior looks stable enough to continue—not whether the trace is a perfectly flat line.
The time required depends on the system’s size and contents. The documentation notes that 50–100 ps is typically sufficient, but that is a guideline, not a pass/fail threshold. If the desired temperature has not been reached or has not stabilized, continue the equilibration rather than treating elapsed time alone as proof of readiness.
If it is not stable yet, continue from the latest results
You can run NVT again using the output from the previous NVT equilibration as the input. This gives you a straightforward next action when the plot is still settling: extend the equilibration, then review the temperature behavior again. Once it is stable enough for your workflow, proceed to NPT to stabilize density.
Check the thermostat settings that matter
The NVT tab provides commonly adjusted parameters such as the integration time step and number of steps. More settings are available through the advanced parameters. For many projects, the documentation suggests velocity rescaling with a stochastic term (v-rescale) and a time constant of about 1 ps. The temperature used for velocity generation should correspond to the temperature coupling reference.
If you use multiple coupling groups—for example, Protein and non-Protein—make sure the number of time constants and reference temperatures corresponds to the number of groups. Position-restraint options are filled automatically based on the input system. For this tutorial, the recommended action is to reset the parameters to their defaults rather than changing settings without a reason.
A quick decision checklist
- Did the run start from the minimized structure or the intended previous NVT result?
- Does the temperature approach the target, and does its running behavior look stable enough to proceed?
- Are fluctuations small and centered around the target rather than a sign that the system has not settled?
- If it is not stable yet, can you continue NVT from the latest result and check again?
For the complete interface walkthrough and related settings, see the NVT Equilibration tutorial.
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