A molecular dynamics system can finish energy minimization and still be far from thermal equilibrium. Starting the next stage too soon may leave you unsure whether the temperature is settling—or whether the simulation simply needs more time. NVT equilibration provides a focused checkpoint: keep the number of particles and volume constant while bringing the temperature toward its target.
The useful question is not whether every temperature reading exactly matches the target. Instead, look at the temperature over time: is its running average approaching the desired value, and does the plot become stable enough to continue? Small fluctuations around the target are normal. A stable-looking trend is more informative than a single reading.
Start with the minimized structure
Before launching NVT, make sure energy minimization has completed and that the minimized system looks reasonable. In SAMSON’s GROMACS Wizard, open the Equilibrate (NVT) tab and provide either the GRO file from minimization (or an earlier equilibration run) or a suitable batch project. If you are continuing from the previous step, the auto-fill control can populate the input path from the previous successful run.
Use defaults as a starting point, not a verdict
The NVT tab provides commonly changed parameters, including the integration time step and number of steps. Other GROMACS molecular dynamics parameters are available through All…. The supplied defaults are intended for typical equilibration runs, but the appropriate settings depend on the system and workflow. For this tutorial, the documented procedure is to reset advanced parameters to their defaults.
One detail worth checking is the relationship between temperature coupling and velocity generation: the temperature specified for generating velocities should correspond to the coupling temperature. For many projects, the documentation describes velocity rescaling with a stochastic term (v-rescale) and a time constant of about 1 ps as a common choice—not a universal rule.
If you couple different groups—for example, Protein and non-Protein—make sure the number of time constants and reference temperatures matches the number of groups. Position-restraint options are filled automatically based on the input system. These details are easy to overlook when changing advanced settings, so check them before starting a run.
Give the temperature time to settle
The time required depends on the system’s size and contents. The tutorial notes that 50–100 ps is typically sufficient, but this is a guide rather than a guarantee. If the running average has not reached a plateau at the target temperature, or the temperature is not yet stable enough for your workflow, continue NVT from the results of the previous NVT run. You do not have to treat the first run as an all-or-nothing test.
You can generate inputs for another environment, run the job locally, or launch it in the cloud. For a local run, progress is shown in the Output window, and jobs can be monitored through Local jobs. When results are ready, you can import the full trajectory, the last frame, or a selected range of frames. The temperature plot is generated with the results; use it to assess the trend rather than judging equilibration from elapsed time alone.
A practical readiness check
- Confirm the input comes from a successful minimization or previous equilibration.
- Check that the target temperature settings are consistent, including the velocity-generation temperature.
- Inspect the temperature plot for a running average that approaches a plateau near the target.
- Allow for small fluctuations; if the temperature is still settling, run additional NVT from the current results.
- Proceed to NPT only once the temperature is stable enough for your workflow.
NVT is a useful checkpoint between minimizing a structure and beginning density equilibration. The key is to use the plot to decide whether the system is ready for the next stage, rather than assuming that a preset duration guarantees stabilization.
For the full walkthrough, see the GROMACS Wizard NVT Equilibration documentation.
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