A molecular dynamics run can be ready to proceed on paper and still leave you wondering whether its temperature is behaving as it should. The system has been minimized, the NVT job has finished—or is still running—and the plot shows fluctuations. Are those normal, or a reason to stop and investigate?
NVT equilibration is the stage where you bring a minimized system toward its target temperature while keeping the number of particles and volume constant. The aim is not to make every point on the temperature trace equal the target. Instead, check whether the temperature’s running behavior settles around the desired value and looks stable enough for the next stage.
Start with the right input
Use the GRO file produced by energy minimization, or the output of a previous equilibration run. If you are continuing from the preceding GROMACS Wizard step, the auto-fill button can populate the input path from the previous successful project. You can also select a GRO file yourself.
Before launching, confirm that the minimized structure looks reasonable and that the minimization output has no unresolved problems. This simple check helps avoid treating an input issue as a temperature-control problem.
Check the settings that matter most
The NVT tab provides common controls such as integration time step and number of steps. GROMACS Wizard supplies default values intended for typical NVT runs, which can be a sensible starting point. The time required depends on the size and contents of the system; the tutorial notes that 50–100 ps is often sufficient, but it is not a guarantee that every system will be ready in that time.
If you inspect advanced settings, pay particular attention to temperature coupling and velocity generation. For many projects, the tutorial suggests velocity-rescaling temperature coupling with a stochastic term (v-rescale) and a time constant of about 1 ps. Make sure the temperature specified for velocity generation corresponds to the coupling temperature.
If you use multiple coupling groups—for example, Protein and non-Protein—the number of time constants and reference temperatures should match the groups. Position-restraint options are populated automatically based on the input system. If you are following the tutorial, reset the advanced parameters to their defaults rather than changing settings without a specific reason.
Read the plot, not just the final number
After the job finishes, inspect the temperature plot. In the tutorial example, the temperature stabilizes around 300 K, the default reference temperature shown there. Small fluctuations around the target are normal. The useful question is whether the running behavior has settled enough to continue—not whether the trace is perfectly flat.
If the temperature has not reached or stabilized around its target, run more NVT equilibration using the current NVT results as input. In other words, extend the equilibration from where the system is now, rather than assuming that one preset duration must work for every system.
Keep the next step in perspective
NVT addresses temperature while volume remains constant. It does not, by itself, establish the density target. Once the temperature is stable enough for your workflow, continue to NPT equilibration to stabilize density. This distinction helps prevent a common source of confusion: a satisfactory temperature plot is a checkpoint for moving on, not proof that every aspect of equilibration is complete.
GROMACS Wizard can generate inputs, run the job locally, or launch it in the cloud. For a local run, progress is available in the Output window and the job can be checked later from Local jobs. Results can be imported as a full trajectory, the last frame, or a selected range. If you cancel the import prompt, the results are not deleted and the plot can still be generated.
For the complete walkthrough and interface details, read the NVT Equilibration documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.