Preparing input files for molecular dynamics (MD) simulations can often feel more complicated than the simulations themselves. If you’ve ever found yourself re-tracing project folders to locate the right .gro file after energy minimization, you’re not alone. This post focuses on a simple yet often overlooked productivity booster in the GROMACS Wizard for SAMSON: automated and flexible input selection for the NVT Equilibration step.
After running the energy minimization step, you need to launch an NVT Equilibration to bring the system to the desired temperature. But how do you efficiently feed the right structure into this next step?
Understanding What You Can Use as Input
The GROMACS Wizard offers two input options for the NVT Equilibration:
- A GRO file – typically the output of a previous energy minimization or equilibration step.
- A batch project – useful if you’re working with scripts or multiple systems in batch mode.
This level of flexibility is helpful, especially when working on larger workflows or troubleshooting issues from a prior simulation.
Save Time with Auto-Fill
If you’re continuing directly from the previous simulation step, the auto-fill button eliminates the need to browse for the correct file:
Click this tiny, but powerful icon to instantly populate the input field with the appropriate path from your last successful run. Whether it’s a GRO file or a batch project, the wizard figures it out for you.
Manual Input Still an Option
If you’re revisiting a simulation or want finer control, the wizard allows manual file selection via the … button next to the input path field. This is particularly useful when testing different simulation branches or re-running previous stages with updated parameters.
Tips for a Smoother Workflow
- Organize your folders: Try to keep each step’s output labeled clearly. Although auto-fill helps, a consistent naming convention still pays off in larger projects.
- Switch between GRO and batch projects: Depending on whether you’re working on individual molecules or automating tasks, being able to use either is a time-saver.
- Don’t forget the file dependencies: If your GRO file depends on another coordinate or topology file, make sure they’re all accessible in your environment.
Why This Matters
Efficient input management keeps your simulation workflow lean and reduces the risk of errors due to incorrect file selection. For teaching, research, or prototyping, these small enhancements in GROMACS Wizard can remove friction and save hours over time.
To learn more on performing NVT Equilibration with GROMACS Wizard, including parameter tuning and result interpretation, visit the full tutorial page: GROMACS Wizard – NVT Equilibration.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.