Before any molecular dynamics simulation can begin, one crucial step stands in the way: preparing the input files properly. For many researchers working with GROMACS in SAMSON, one common source of frustration is figuring out what input the NVT Equilibration step actually needs—and what to do when it’s not accepted.
In this blog post, we take a closer look at this often-overlooked setup phase and show how a few simple choices can make your workflow smoother and more reliable.
Choosing an Input for NVT Equilibration
Once your system in SAMSON has been energy-minimized, the next step in your MD workflow is typically the NVT Equilibration. In this phase, the system is brought to the right temperature while keeping its volume constant. But what should you give the GROMACS Wizard as input?
You have two options:
- A GRO file generated from the Minimization step or a previous equilibration run.
- A batch project that includes a minimized system. This is especially useful when working in a pipeline or using automated batch setups.
Simplified Input with Auto-Fill
The GROMACS Wizard in SAMSON includes a handy feature that reduces manual mistakes: the auto-fill option. This button (see below) automatically retrieves the appropriate file from the previous pipeline step, saving you time and preventing common missteps like selecting the wrong GRO file.
If you prefer full control or want to test a different configuration, you can also manually point to a GRO file using the … button.
When to Reuse an Equilibration Output
If your simulation didn’t reach the expected temperature plateau, SAMSON allows you to re-run NVT Equilibration using the output of a previous NVT run—without manually digging for the right file paths. Simply click on the auto-fill button again, and the Wizard pre-fills the most recent results.
Using Batch Projects as Input
If you’re running batch simulations, choosing a batch project as the input is efficient. SAMSON keeps all relevant files bundled and paths correctly traced, which reduces the risk of broken file links or incorrect configurations when moving between steps such as Minimization > NVT > NPT > Production.
For more on setting batch projects in SAMSON, see the Batch Computations tutorial.
Small Actions, Big Stability
It may feel tempting to copy and paste an input path or speed through this step to get to simulation results faster. But choosing the correct and consistent input structure sets the stage for stable, interpretable simulations. Leveraging SAMSON’s auto-fill and structured project handling minimizes points of failure and repetitive manual work—so you can focus more on your system and less on setup errors.
To explore the full process and options, visit the official documentation on NVT Equilibration in GROMACS Wizard.
SAMSON and all SAMSON Extensions are free for non-commercial use. To get started with SAMSON, visit www.samson-connect.net.