One common obstacle faced by molecular modelers when working with molecular dynamics (MD) simulations is managing input files correctly between simulation stages. If you’ve ever had to rerun an NPT equilibration in GROMACS just because you didn’t set the right input file path—or worse, forgot what the correct file was—you’re not alone.
With the GROMACS Wizard in SAMSON, this issue is handled much more elegantly. The input selection step in NPT equilibration offers a streamlined way to avoid file path mistakes and reduce the time you spend managing files manually.
Autofill: Your Shortcut to the Right File
If you’re running multiple simulation steps sequentially—such as energy minimization, NVT equilibration, followed by NPT equilibration—accurately selecting the correct structure output is key. In the GROMACS Wizard, you don’t need to browse your file system each time. Instead, you can simply use the auto-fill button that automatically sets the path to either the latest GRO file or the batch project resulting from the previous successful step.
This small but impactful feature minimizes human error, especially in large or repetitive simulation pipelines. It also helps junior modelers who might not yet fully understand the sequence and dependencies of simulation steps.
Prefer Manual Selection? No Problem
For those who prefer to be thorough or are working on branched workflows, there’s also an option to manually select the input .gro file or project. Click the … button and navigate to your preferred file. Just make sure it originates from a minimized or equilibrated structure—whether from NVT equilibration or a previous NPT run.
Why This Matters
Incorrect input can lead to misleading simulation results or wasted compute resources. Choosing the right input structure is essential to ensure physical consistency across simulation stages. By automating this step or making it more transparent, SAMSON’s GROMACS Wizard helps modelers stay focused on designing and analyzing their systems—not debugging input file mismatches.
To learn more about this step in the SAMSON workflow, visit the full tutorial page for NPT Equilibration.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.