A temperature trace that moves up and down can make it hard to tell whether an NVT equilibration has worked. Should you stop, run longer, or move on? The useful signal is not a perfectly flat line: small fluctuations around the target temperature are normal. What you are looking for is a running average that reaches a plateau near the target and stays stable enough for your workflow.
What NVT is—and what it is not
NVT keeps the number of particles, volume, and temperature constant. In this stage, the practical goal is to bring the system to its target temperature in a controlled way. It does not stabilize density; that is the purpose of the subsequent NPT equilibration step.
This distinction helps avoid a common source of uncertainty: a successful-looking temperature plot is a reason to continue to NPT, not evidence that every aspect of the system is equilibrated.
Start from the right input
Use the GRO file from energy minimization or from a previous equilibration run. If you are continuing the workflow in GROMACS Wizard, the auto-fill button can populate the input path from the previous successful project. You can also select a GRO file yourself, or provide a suitable batch project.
Before starting, make sure the minimized system looks reasonable and that the minimization output has no unresolved problems. Equilibration is not a substitute for addressing issues in the starting structure.
Choose settings with the temperature trace in mind
The NVT tab provides commonly adjusted settings, including the integration time step and number of steps. The appropriate run time depends on the system’s size and contents. As a typical guide, 50–100 ps may be sufficient, but the plot—not the elapsed time alone—should inform your decision. If the target has not been reached or the temperature has not stabilized, run additional NVT equilibration using the results of the previous NVT run.
In the advanced temperature-coupling settings, the thermostat, coupling groups, time constant, and reference temperature can be adjusted. For many projects, the documentation gives velocity rescaling with a stochastic term (v-rescale) and a time constant of about 1 ps as a typical choice. Check that the velocity-generation temperature 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 number of groups. Position-restraint options are filled automatically based on the input system. For a tutorial run, reset parameters to their defaults unless you have a reason to customize them.
Read the plot, not just the job status
After the job finishes and results are loaded, GROMACS Wizard generates a temperature plot. Compare the trace with the target value, and look for a running behavior that has settled around it. Small fluctuations are expected; an unsettled trend or a temperature that has not reached the target is a reason to continue equilibration rather than move on automatically.
Results can be run locally, prepared as inputs for another machine, or launched in the cloud. For local runs, progress is available in the Output window and the Local jobs list. When importing results, you can choose to bring in the whole trajectory, the last frame, or a range of frames. If you cancel the import, the results are not deleted, and the plot can still be generated.
A quick decision checklist
- Did the run start from a reasonable minimized structure or the latest NVT results?
- Does the temperature approach the intended reference value?
- Has its running behavior settled enough to continue, allowing for normal fluctuations?
- If not, can you extend equilibration by launching another NVT run from the current results?
Once the temperature is stable enough for your workflow, continue to NPT equilibration to work toward stabilizing density. For the full procedure and interface details, read the NVT Equilibration tutorial.
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