Equilibration in molecular dynamics is an essential step before launching production simulations. But even experienced molecular modelers sometimes hit snags during the NVT (constant particle number, volume, and temperature) equilibration phase. This blog post explores how to avoid common setup issues during this step using the GROMACS Wizard in SAMSON, and how to make sure you’ve stabilized your system the right way.
Why is NVT equilibration challenging?
It’s often overlooked how sensitive this step can be. Selecting the wrong input structure, mismatching parameters, or misunderstanding how temperature coupling works may lead to simulations that look fine—but are, in fact, unstable or unreproducible. SAMSON’s GROMACS Wizard provides tools that make this process more intuitive, if you know where to look.
1. Choosing the Correct Input: Minimization First
Before NVT can begin, your system must be minimized. This ensures that you are not starting from a structure with absurd clashes or distorted geometries. In GROMACS Wizard, select either a GRO file from previous minimization or a batch project using the dedicated input section, as shown here:
You can use the auto-fill button to automatically select the most recent compatible file, saving you navigation time and reducing the chance of misconfiguration.
2. Temperature Coupling: One Setting Doesn’t Fit All
The temperature coupling method affects how the simulation matches the system’s kinetic energy to the desired temperature. By default, SAMSON uses velocity rescaling (v-rescale), which suffices for many systems. But for specialized setups—like splitting a system into protein and solvent groups—you must define separate coupling parameters for each group:
You can add these groups directly from the NVT tab using the Edit index groups button after loading your system.
3. Check for Stabilization Visually
A frequent pain point is not being sure whether your system actually reached the desired temperature. In GROMACS Wizard, a plot of temperature vs. time is automatically generated once the calculation finishes and results are loaded. If your system doesn’t stabilize (i.e., you don’t observe a roughly horizontal line), rerun the NVT equilibration using the output GRO file as a starting point.
This visual feedback provides quick insight into whether additional refinement is needed before proceeding to NPT equilibration.
4. Save, Load, and Reset Parameters Easily
If you’ve spent time configuring parameters for one system and would like to reuse them, you can save them as an MDP file. This makes your workflow more reproducible across projects. Similarly, if things become messy, the Reset button restores defaults, preventing configuration paralysis.
These small interface features—combined with automatic input handling and job tracking—make the GROMACS Wizard in SAMSON a practical solution to one of the more subtle yet vital steps in molecular simulation.
To learn more about NVT equilibration in SAMSON’s GROMACS Wizard, visit the full documentation page:
https://documentation.samson-connect.net/tutorials/gromacs-wizard/nvt-equilibration/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.