Molecular dynamics (MD) simulations often involve long workflows composed of successive stages: minimization, temperature equilibration (NVT), pressure equilibration (NPT), production runs, and post-analysis. Each step builds on the previous one. However, a frequent frustration among modelers—especially those new to MD with GROMACS—is simply using the wrong input structure when launching NPT equilibration. This mistake can lead to inaccurate results or simulation failures.
If you’ve ever asked yourself, “Where do I load the input file from, again?”, you’re not alone. GROMACS Wizard in SAMSON provides a clean, interactive way to manage MD workflows, but ensuring proper input selection is still critical. In this blog post, we explain how to correctly set the input for the NPT equilibration step—and how to avoid those pesky simulation misfires. 😅
Why Input Structure Selection Matters
NPT (constant Number of particles, Pressure, and Temperature) equilibration is meant to stabilize the system’s pressure and density after your temperature has already been equilibrated under NVT. This means your input must reflect a system that has already been minimized and equilibrated at the desired temperature.
In GROMACS Wizard, this translates to choosing either:
- A GRO file generated from a previous step (minimization or NVT).
- A batch project already processed through at least the NVT step.
Streamlining Input Selection
You could manually browse for the GRO or batch project file, but there’s a better way: just use the Auto-Fill button (
). This feature picks up the output from your last completed step and automatically uses it as input for the NPT step.
Prefer manual control? That’s okay too. Click the … button and locate the file on your own. Just ensure it corresponds to the right step in your simulation pipeline.
Tip: Understand the File Flow
A common pitfall is selecting a file that hasn’t gone through both minimization and NVT. This breaks continuity and potentially leads to unstable NPT runs. As a rule of thumb:
- Start with a minimized structure → Minimization step.
- Equilibrate temperature → NVT Equilibration.
- Then stabilize pressure → NPT Equilibration.
The input to NPT must come from step 2 (or even from a first NPT attempt if you’re doing a second run).
Bonus: Batch Computation Compatibility
If you’re using GROMACS Wizard’s batch processing, note that you can select a whole batch project with a history of preprocessing. The software understands where in the pipeline it is, making batch runs much easier to manage correctly.
Final Check
Still unsure? Once your file is loaded, take a quick look at trajectory metadata (step suffix, timestamp) and confirm it matches the stage of the workflow. Then proceed with confidence!
To learn more about setting inputs and running NPT equilibration in SAMSON’s GROMACS Wizard, visit the full documentation page here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at samson-connect.net.