When Default Isn’t Enough: How to Use Your Own GROMACS Version in SAMSON

For many molecular modelers, reproducibility and performance optimization are more than just desirable — they’re essential. While the GROMACS Wizard integrated in SAMSON offers one of the latest versions of GROMACS by default, there are valid reasons why researchers may want to work with a custom installation of GROMACS instead.

Whether you’re aiming for strict reproducibility using a legacy version, or you simply want to leverage a GROMACS build optimized for your specific hardware, SAMSON makes it possible to switch to a local GROMACS installation with just a few steps. This is especially relevant for users who have invested time tuning their GROMACS setup or managing shared compute environments where specific versions are mandated.

Why switch GROMACS versions?

Here are some reasons to configure SAMSON’s GROMACS Wizard to use a locally installed version of GROMACS:

• You are working in a shared computing environment where a specific GROMACS version is enforced.
• You’ve compiled GROMACS with hardware-specific optimizations.
• You want results to be consistent with past studies that used a different GROMACS release.
• You need to use GROMACS features that are not available in the default bundled version.

How to do it

Switching to your own version of GROMACS in SAMSON is as simple as adjusting two file paths:

1. Open the Settings panel in the GROMACS Wizard.
2. Enable the checkbox labeled Use a different GROMACS version.
3. Specify:
   • The path to your local GROMACS executable (gmx or gmx.exe).
   • The path to the folder containing your GROMACS force fields (typically $HOME/gromacs/share/top/).

For example, on Linux or macOS, you might point to:

Once set, SAMSON will validate whether the executable is recognized. If successful, the selected GROMACS version will be displayed. If not, SAMSON will show “invalid”, enabling you to double-check your paths.

Good to know

• You can still use the SAMSON-supplied version if needed, simply by deselecting the custom option.
• This configuration affects local computations only, not SAMSON Cloud jobs, which use a managed version of GROMACS.

Importantly, if you switch to a version of GROMACS with different behavior or constraints, be sure to validate early steps like energy minimization or equilibration with test runs. This helps catch differences in defaults or file parsing behaviors between versions.

Switching to a specific GROMACS version offers flexibility and control to more advanced users, and it integrates smoothly within the broader SAMSON workflow. Want to know more about other settings? Learn more in the full documentation here: https://documentation.samson-connect.net/tutorials/gromacs-wizard/settings/

SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.