Running molecular dynamics (MD) simulations may sound routine, but if you’ve ever seen unstable temperatures, crashing systems, or hours of lost compute time, you know how crucial getting equilibration right is. One often overlooked challenge is setting up the NVT equilibration phase properly.
NVT equilibration, or constant Number of particles, Volume, and Temperature, is a vital step to stabilize temperature before continuing simulations under production or different ensembles. It’s especially helpful to avoid unrealistic dynamics occurring from unrelaxed systems after energy minimization.
Start With the Right Input
The first step in SAMSON’s GROMACS Wizard is selecting the right input file for your NVT run. Did you already finish energy minimization? If yes, your input can either be:
- A .gro file output from the energy minimization
- Or a project file from earlier minimization or equilibration steps
Use the auto-fill button to automatically retrieve the correct path—avoiding human error and saving time during setup.
Choosing Smart Parameters
Not sure how long to run your NVT equilibration? For typical systems, 50–100 ps often does the trick, but check carefully whether the temperature stabilizes. Use the Parameters section to set timestep and number of steps, and explore advanced options via the All… button.
One priority: Temperature coupling. This defines how temperature is controlled. The v-rescale thermostat (velocity rescaling with a stochastic term) with a time constant around 1 ps is usually a good default.
For multi-component systems, such as protein in solvent, you can apply separate temperature coupling to different groups. For instance:
Remember: the number of coupling groups must match the number of reference temperatures and time constants. You can define custom groups via the Edit index groups button.
Run Locally or in the Cloud
Once you’re ready, SAMSON gives you flexibility in how you run the simulation. Choose:
- Generate inputs for running elsewhere (e.g., a cluster), or
- Equilibrate locally using your PC, or
- Equilibrate in the cloud if local compute is limited.
Check the Temperature Plot
After running the NVT equilibration, the GROMACS Wizard shows you a plot of temperature over time. This quickcheck helps validate whether the system has become thermally stable around your target temperature (usually 300 K).
If the temperature hasn’t equilibrated, don’t panic. You can simply re-run the equilibration using output from the previous NVT step—just click auto-fill and go.
Checking this plot is far better than relying on log files alone, and you can even export it for your records or publication.
Conclusion
Taking the time to correctly set up NVT equilibration can save significant effort down the line. By using smart defaults, creating separate coupling groups when relevant, and checking diagnostic plots, you’ll avoid many common headaches encountered by even seasoned molecular modelers.
Want to dive deeper into each detail? Read the full documentation here: GROMACS Wizard – NVT Equilibration
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get it at https://www.samson-connect.net.