One of the most frequent and frustrating roadblocks in molecular dynamics simulations is getting the input right. Whether you’re a graduate student running your first simulation or a seasoned researcher working on a complex biomolecular system, mistakes in selecting input files and setting up parameters for stages like NVT equilibration can slow you down considerably.
In SAMSON’s Integrative Molecular Design Platform, the GROMACS Wizard simplifies many parts of the simulation setup. But when it comes to the NVT Equilibration step, a common source of confusion is how to select the right input structure — especially when juggling multiple simulation steps and their outputs.
What Kind of Input Does NVT Equilibration Need?
The NVT step requires a structure that has already been prepared and minimized. You can provide either:
- A GRO file generated from the energy minimization step or previous NVT simulations.
- A batch project that contains the necessary data from earlier steps.
If you’ve just completed the Minimization step, it makes sense to directly use its output. But locating the correct file path manually every time can be tedious — not to mention error-prone, especially if you store multiple runs in your workspace.
Let SAMSON Help: Auto-fill Your Input
Thankfully, SAMSON includes an auto-fill function that pulls the correct output files from the previous step automatically. Just click this button:
and it will populate the input field correctly, sparing you from file path errors or selecting outdated data by mistake.
If, for any reason, you want to pick a different file, you can still do so manually using the … button. This makes it easier for users who like to organize folders differently or test with alternate inputs.
Why Is This Important?
Input errors during simulations don’t always produce immediate warnings. You might run your simulation only to realize hours or even days later that you were using the wrong starting geometry. The impact can be subtle — shifts in calculated temperature, misaligned atoms, lost restraints — which affect the accuracy of the results and may require full reruns.
This small but practical feature in SAMSON’s GROMACS Wizard allows you to streamline reproducibility. It also encourages better workflow hygiene by making sure that your simulations use well-connected, verified input chains from previous steps.
Bonus Tip: Batch Projects
If you’re managing simulations across different conformations or running long equilibration chains, consider working with batch projects. These are especially helpful when using the cloud feature or organizing large datasets. The auto-fill feature works with batch jobs too, reducing management overhead.
In a field where a misstep in setup can cost you hours of compute time, automating and verifying your input setup is worth the few seconds saved — and then some.
To learn more about NVT equilibration in SAMSON’s GROMACS Wizard and other useful simulation tips, visit the full documentation here: 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.