Molecular modelers often rely on precise control over their simulation environments — for reasons ranging from reproducibility to compatibility with previous work or external tools. One recurring issue is being forced to use a default GROMACS version bundled within software, especially when a custom build is already installed and validated locally. If this sounds familiar, and you’re using the GROMACS Wizard in SAMSON, there’s good news — you can specify and switch to your own GROMACS installation.
The GROMACS Wizard comes with a pre-shipped version of GROMACS that works out-of-the-box. However, it also includes an option to override this and run simulations with a custom GROMACS installation on your system. This capability removes a significant reproducibility barrier, especially when fine-tuning performance or integrating workflows based on specific GROMACS versions.
Why use a custom GROMACS installation?
- You need to ensure **reproducibility** of published results using a specific GROMACS version.
- You have a version compiled with custom flags or GPU acceleration.
- Your institution or collaborator enforces version consistency across compute clusters.
To use your local GROMACS version in the GROMACS Wizard, click the Settings button at the top of the interface:
Then, in the settings panel, activate the option “Use a different GROMACS version”. Two inputs are required:
- GROMACS executable path: Select the
gmxexecutable (typically found in/usr/local/gromacs/bin/or in your conda/compiled environment). Use the folder icon to browse your system. The GROMACS Wizard will display the detected version or flag it as unrecognized if invalid. - Force fields directory: Provide the folder that contains all the
forcefield.ffsubfolders (e.g.,$HOME/gromacs/share/top/). This ensures correct force field availability.
Once set up, all local computations will run using your selected GROMACS version. This helps ensure consistency with other pipelines and removes potential discrepancies due to version regressions.
Important note on compatibility
GROMACS Wizard reads metadata from the executable to ensure it is valid. If your custom GROMACS doesn’t expose the correct version or metadata (e.g., stripped executable), you may see an “invalid” warning. Make sure your build is complete and functional when used independently on your terminal.
What about the Cloud?
This custom version option applies only to local jobs. Any simulations sent to the Cloud via GROMACS Wizard will still use the bundled version maintained remotely.
Switching to a custom GROMACS version expands your control over simulation fidelity and aligns your modeling environment with your research needs. Whether it’s for performance, reproducibility, or simple preference, this small feature can address a significant need in molecular simulation work.
To learn more, visit the official documentation page: GROMACS Wizard Settings Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.