A molecular dynamics run can be ready to launch and still leave you wondering: has the system actually reached its target temperature? A temperature trace that moves up and down is not automatically a problem—small fluctuations are normal—but continuing too early can make it harder to judge what happens in the next stage.
NVT equilibration is the controlled step between energy minimization and density equilibration. The ensemble keeps the number of particles and volume constant while temperature is controlled. The practical goal is not a perfectly flat line: it is for the temperature to fluctuate around its target and for its running behavior to become stable enough to proceed.
Start from a sound minimized system
Before launching NVT, complete energy minimization and check that the system looks reasonable and that the minimization output does not show unresolved problems. NVT is not a replacement for fixing an unsuitable starting structure. It begins from the minimized structure—or from the results of an earlier equilibration run.
In SAMSON’s GROMACS Wizard, open the Equilibrate (NVT) tab. The input can be a GRO file from minimization or a previous NVT run, or a suitable batch project. If you are continuing from the previous step, the auto-fill button can populate the input path from the previous successful project. You can also select a GRO file yourself.
Set the temperature controls consistently
The Wizard provides default NVT parameters for typical runs, with commonly adjusted settings such as the integration time step and number of steps available in the main Parameters section. Other GROMACS options are available through All…, where you can inspect or change advanced settings.
Pay particular attention to temperature coupling. The documentation notes that velocity rescaling with a stochastic term (v-rescale) and a time constant of about 1 ps are typical choices for many projects. The temperature used for velocity generation should correspond to the coupling temperature. If you use more than one temperature-coupling group—for example, Protein and non-Protein—make sure the time constants and reference temperatures match the groups you have defined. For many workflows, the default System group is the straightforward starting point.
Position-restraint options are filled automatically based on the input system. For this tutorial, the suggested approach is to reset the parameters to their defaults rather than changing settings without a specific reason. You can also reset, load parameters from an MDP file, or save them for reuse.
Give the system time—and judge the trend
The time required depends on the system’s size and contents. The tutorial gives 50–100 ps as a typical duration, not a guarantee that every system will be equilibrated within that window. The useful question is whether the running average of the temperature reaches a plateau near the target value. A trace can have ordinary fluctuations and still be stable enough to continue; a trend that has not settled is a reason to run longer.
When the results are available, inspect the temperature plot in the Plots section. In the tutorial example, the temperature stabilizes around 300 K, the default target shown in the advanced parameters. If it has not reached or stabilized around the desired value, run NVT again using the previous NVT results as input. This lets you extend equilibration from the current state instead of treating the first run as an all-or-nothing attempt.
Launch and review the results
You can generate project inputs, equilibrate locally, or launch the job in the cloud. For a local run, choose Equilibrate locally; progress is shown in the Output window, and job status remains accessible through Local jobs. Once the calculation finishes, you can import the full trajectory, only the last frame, or a selected range, and choose periodic-boundary-condition treatment and centering options. Canceling the import does not delete the results, and the plot can still be generated.
Before moving on, confirm that the temperature fluctuates around the target and that its running behavior looks stable enough for your workflow. Then continue to NPT equilibration, where the next goal is to stabilize density. For setup details and the complete walkthrough, learn more in the NVT Equilibration documentation.
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