One common challenge faced by many molecular modelers is ensuring reproducibility and compatibility between different simulations, especially when working across teams or reproducing results from published work. Since software like GROMACS evolves rapidly, slight version mismatches can generate inconsistencies in workflows or results—even when using the same input files.
Thankfully, SAMSON’s GROMACS Wizard allows you to sidestep that issue by using your own local version of GROMACS, instead of the version shipped with the GROMACS Wizard. This small detail could save you hours of troubleshooting incompatible parameters or unexplained simulation warnings.
Why Use a Custom Version?
You might already have a specific version of GROMACS installed—maybe it’s optimized for your machine, or it’s the same version your collaborators are using. With SAMSON, you can easily configure the GROMACS Wizard to work with your preferred version, giving you consistency and control.
How to Set It Up
To select your own version of GROMACS, open the GROMACS Wizard panel inside SAMSON and click the Settings button at the top:
In the Settings window, locate the option labeled Use a different GROMACS version. After checking that box, you’ll need to provide two file paths:
- The GROMACS executable – usually named
gmx.exeon Windows orgmxon Linux/macOS. Use the folder browser icon to select the location. SAMSON will validate the file and display the version number if recognized. - The force fields folder – where GROMACS keeps its
.fffolders, typically in $HOME/gromacs/share/top/ or similar. This is necessary so that the Wizard can access the force fields your version of GROMACS supports.
Pitfalls and Precautions
Keep in mind that if the GROMACS executable you select is not recognized by SAMSON, it will display an invalid message, and you won’t be able to proceed. In that case, double-check that you’re selecting the right binary, and that it is accessible from your user account.
Also, make sure the corresponding force field folders are really compatible with the selected version. Mismatched force field files may lead to unintended simulation outcomes.
When This Matters Most
Here are a few situations where using your own GROMACS version can really make a difference:
- Re-running simulations from older publications that specify an exact GROMACS version
- Using patches or experimental features not present in the standard release
- Ensuring consistency across simulations run on different machines (e.g., local desktop and HPC cluster)
This flexibility makes the GROMACS Wizard in SAMSON not just useful for beginners, but also convenient for experienced modelers who need tight control over their simulation environments.
To learn more about supported options and performance tuning settings, visit the full documentation at https://documentation.samson-connect.net/tutorials/gromacs-wizard/settings/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.