Preparing molecular systems for simulations typically involves several steps, and one of the persistent pain points for many molecular modelers is selecting the correct input files at each stage—especially during equilibration.
Do you find yourself digging through folders, unsure which .gro file to use for your NVT equilibration in GROMACS? You’re not alone. Running a molecular dynamics simulation should not start with a scavenger hunt.
Why choosing the right input matters
In the context of NVT equilibration, the correct input structure is essential. It must come from a system that was properly minimized or previously equilibrated. Using the wrong file can result in simulation failures or outputs that are physically meaningless.
How GROMACS Wizard in SAMSON helps
The GROMACS Wizard Extension in SAMSON offers several streamlined options to make this step much easier—and avoid mistakes that can cost hours of computing time.
Option 1: One-click auto-fill from previous steps
If you’re following the GROMACS Wizard workflow, there’s a good chance you’ll already have completed the energy minimization step. In that case, simply click on the auto-fill button:
This automatically fills the input path using either the resulting .gro file or the batch project from your last successful step. It saves time and greatly reduces the chance of mistakes.
Option 2: Manual file selection
If for any reason you prefer to manually select your file, you can do that easily using the … button in the input section.
Whether you’re using a standalone .gro file or a full batch project, the interface guides you through the process, making sure that the file you’ve chosen is compatible with the equilibration task at hand.
Loading your system before editing index groups
Another useful hint: If you’re planning to customize index groups, be sure to first load the system by clicking “Load” next to your chosen input. This makes options like Edit index groups available.
Why this matters
Efficient and reliable input selection is crucial in a simulation pipeline. With the SAMSON GROMACS Wizard, you’re less likely to hit dead ends caused by wrong or missing inputs. Even better—you get to focus on science instead of file management.
You can explore more on this topic and see how to proceed with parameter setup and simulation launch by visiting the full documentation page: NVT Equilibration.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.