One of the most common frustrations among molecular modelers using GROMACS is the seemingly simple—but often error-prone—task of selecting the correct input structure when launching production Molecular Dynamics (MD) simulations. It might happen that after spending hours on system setup and equilibration, a job fails to start or delivers misleading results due to a small oversight in choosing the right input file.
In the GROMACS Wizard from SAMSON, a key feature simplifies this critical step. Here’s how to avoid mistakes and streamline your workflow when moving from equilibration to production MD.
Choosing the Right Structure: GRO vs Batch Project
When launching the Production MD step, you need to input either a GRO file or a batch project that has already gone through NPT equilibration:
- GRO file: Typically the output from the previous NPT equilibration or a previous production MD run.
- Batch project: Useful when managing multiple simulations at once. These should also originate from equilibrated systems.
Unclear file paths or a simple mismatch between equilibration and production setups can bring everything to a halt.
Auto-Filling the Previous Step
To minimize room for error, GROMACS Wizard includes an “auto-fill” button that allows users to import the correct file path from the previously successful step with one click.
Click the auto-fill button to retrieve the correct input path instantly.
This saves time and reduces the risk of selecting an outdated or incorrect file. The path can point to either:
- The .gro file from NPT equilibration or previous MD steps, or
- A batch project location.
Prefer Manual? Still Covered
If you’re customizing your workflow or running external scripts, you can opt to manually select the .gro file by clicking the … button. This provides flexibility while still integrating smoothly with the rest of the SAMSON pipeline.
Why This Matters
Incorrect input structures can lead to failed simulations, missing files, or inaccurate physical results. Worse yet, issues might appear hours later during analysis, making them much harder to trace. Proper input management—whether automated or manual—is essential for a successful Production MD run.
The integration of auto-fill functionality in SAMSON’s GROMACS Wizard directly addresses this substantial pain point—especially for users who run multiple simulations or return to projects after a break. It’s a small step that contributes to significantly smoother molecular modeling workflows.
To learn more about running Production MD simulations using the GROMACS Wizard, consult the full documentation at https://documentation.samson-connect.net/tutorials/gromacs-wizard/production-md/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.