A minimized molecular system is not automatically ready for the next stage of a molecular-dynamics workflow. Before adjusting density or moving on to production simulation, you need to bring the system to its target temperature and check that its behavior is stable enough to continue. That checkpoint can be surprisingly easy to misread: molecular temperatures fluctuate, and a noisy trace does not necessarily mean the equilibration has failed.
NVT equilibration is the first part of a common two-stage equilibration process. The number of particles and the volume are held constant while temperature is controlled. Once temperature is stable, an NPT step can be used to stabilize density. Here is a practical way to approach that transition with GROMACS Wizard.
Start with the right input
Begin from the result of energy minimization, or from the output of an earlier NVT run if you need to continue equilibration. In the Equilibrate (NVT) tab, use the auto-fill control to populate the input path from the previous successful step, or choose the relevant GRO file yourself. If you are working with a batch project, that can also be used as input.
Before launching the job, check that the minimized structure looks reasonable and that the minimization output has no unresolved problems. Equilibration is not a substitute for addressing issues in the starting structure.
Choose parameters with a clear goal
The main goal of this stage is not to make every temperature reading identical. Instead, look for the running average to approach a plateau near the target temperature. Small fluctuations around the target are normal. The appropriate simulation duration depends on the size and contents of the system; the tutorial notes that 50–100 ps is often sufficient, but this is a guide rather than a guarantee.
The NVT tab provides commonly adjusted settings, including the integration time step and number of steps. More advanced GROMACS parameters are available through All…. For many projects, the default settings are a useful starting point. If you change temperature coupling, keep the velocity-generation temperature consistent with the coupling reference temperature. The documentation describes v-rescale with a time constant of about 1 ps as a common choice for many projects; the appropriate settings still depend on your system and workflow.
Position-restraint options are filled automatically based on the input system. If you need separate temperature-coupling groups—for example, protein and non-protein components—select the available index groups and make sure the number of time constants and reference temperatures matches the number of groups. If you are unsure which custom settings are appropriate, reset to the defaults rather than changing parameters without a specific reason.
Run, then evaluate the trend
You can generate inputs for another environment, run locally, or launch a cloud job. For a local run, select Equilibrate locally. The Output window reports progress, and the Local jobs button lets you check job status while continuing to use SAMSON.
After a single project finishes, you may be prompted to import results. You can import the full trajectory, only the last frame, or a selected range, and choose how periodic boundaries are treated and what the system is centered on. If you cancel the import, the results are not deleted; the temperature plot can still be generated.
Use the plot as a trend check: has the running behavior settled around the target, or is it still moving toward it? If temperature has not stabilized, continue NVT from the current NVT results rather than restarting from the original minimized structure. Repeat as needed, then proceed to NPT when the temperature behavior is stable enough for your workflow. This keeps the decision focused on the simulation evidence instead of an arbitrary expectation that every trace should look perfectly flat.
For the complete workflow and interface details, see the GROMACS Wizard NVT Equilibration tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.