When and Why to Use Your Own GROMACS Version in SAMSON

If you’re a molecular modeler using GROMACS for simulations, you probably know how important reproducibility and computational optimization can be. While SAMSON’s GROMACS Wizard comes bundled with a recent GROMACS version ready for cloud and local jobs, there are cases where switching to a custom version of GROMACS is not only desirable—it may be essential.

Why use a different GROMACS version?

There are a few common motivations:

  • Reproducing published results: If a paper used a specific GROMACS version, matching that setup helps ensure consistency.
  • System-specific optimization: Some institutional computing environments already have optimized GROMACS builds that make better use of available hardware.
  • Consistency across projects or collaborators: Teams may standardize on a particular version.

How SAMSON makes it easy

The GROMACS Wizard in SAMSON offers a simple interface to switch to a different local version of GROMACS. Just follow these steps:

1. Click the Settings button in the GROMACS Wizard.

Open settings

2. In the settings panel, check the option Use a different GROMACS version.

Custom GROMACS path

3. You’ll need to specify two paths:

  • The GROMACS executable: Choose the path to gmx (Linux/macOS) or gmx.exe (Windows). SAMSON will detect and display the version so you can verify it’s correct.
  • The force fields folder: This is typically where folders like amber99sb.ff or gromos54a7.ff are stored—e.g., $HOME/gromacs/share/top/.

Things to watch for

  • If the executable path is invalid or unrecognized, SAMSON will flag it as “invalid.” Double-check the location and version.
  • Make sure your selected version is compatible with your input files and any topology or force field files you plan to use.

Whether you’re preparing a publication, working on a shared system, or just prefer to use a known environment, this little-known feature can save you time and ensure reproducibility across runs.

To dig deeper into how to configure this and explore other simulation settings, visit the full documentation page: GROMACS Wizard – Settings.

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

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