If you’ve ever run a molecular dynamics simulation only to see your system blow up 🔥 right after energy minimization, you’re not alone. One of the most frequent issues molecular modelers face is rushing into full simulations without proper temperature equilibration. Skipping or mishandling this step often results in nonphysical behavior, corrupted trajectories, or failed long-term simulations.
The good news? NVT equilibration — a procedure to stabilize temperature while holding the number of particles and volume constant — is easy to set up using the GROMACS Wizard in SAMSON. In this post, we’ll walk through how to handle this crucial step inside the intuitive interface of SAMSON’s GROMACS Wizard, ensuring your simulations begin with a robust and stable foundation.
Why NVT Equilibration Matters
Before launching production-level molecular dynamics simulations, you need to bring your system to the desired temperature — often around 300 K — and stabilize kinetic energies. This is achieved through an NVT ensemble (Canonical ensemble), which maintains a constant number of particles, volume, and temperature. It allows the system to thermally relax without introducing volume fluctuations too early.
Setting the Stage: Input Structures
Once energy minimization is complete, you can kick off NVT equilibration directly from the GROMACS Wizard’s NVT Equilibration tab. If you’ve just run a minimization, hit the Auto-Fill button to automatically link to the output GRO file of the minimization step.
Controlling the Variables: Temperature Coupling
In GROMACS, temperature control is handled via thermostats. A commonly used method is velocity rescaling with a stochastic term (v-rescale). In SAMSON’s GROMACS Wizard, this setup is straightforward. You can modify the thermostat type, time constants, groups to be coupled, and reference temperature directly via the graphical interface.
You can even define custom index groups (e.g., Protein / Non-Protein) if you want different parts of your system to be controlled separately. Just load your system using the Load button and then launch the index group editor.
Launching and Monitoring the Equilibration
Once parameters are set, you can launch the NVT equilibration locally, in the cloud, or generate inputs for another computing environment. The local option is convenient and allows continued use of SAMSON during the simulation thanks to background job management.
Progress can be tracked in the Output window, and once complete, you’ll be prompted to import results. You can download entire trajectories, select specific frames, or skip the import and just examine generated plots.
Visual Feedback: Interpreting Temperature Plots
SAMSON automatically generates a temperature plot showing average temperature over time. It should plateau around your target (e.g., 300 K). Any large fluctuations might indicate the need for longer equilibration runs or parameter adjustments.
What If the Temperature Doesn’t Stabilize?
This is a common concern. No worries — you can relaunch NVT equilibration using outputs from the previous run. Just reselect the updated GRO file with the Auto-Fill button and run the step again. Equilibration typically takes 50-100 ps to stabilize but could require longer for large or complex systems.
With a properly equilibrated system, you’re ready to transition to the next phase: NPT Equilibration.
To learn more, see the full documentation on NVT Equilibration in GROMACS Wizard.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.