When It Matters: How to Use Your Own Version of GROMACS in SAMSON

Switching between different versions of GROMACS isn’t just a technical preference—it’s often a necessity for molecular modelers. Whether for ensuring reproducibility, taking advantage of specific performance improvements, or simply using a cluster’s precompiled GROMACS, being able to control the version you use is critical.

If you’re a molecular modeler using SAMSON‘s GROMACS Wizard, there’s a simple but powerful feature that allows you to rely on your own local installation of GROMACS instead of the built-in one. This can make a big difference when working in controlled computing environments or when using force fields that require specific versions for compatibility.

Why choose a custom GROMACS version?

  • Reproducibility: Scientific publications often require simulations to be traceable to a specific GROMACS version.
  • Compatibility: Some workflows or extensions might only support certain GROMACS versions.
  • Performance: Custom builds optimized for your hardware may outperform the general-purpose versions packaged in tools.

Enabling your own GROMACS in SAMSON

To use your local GROMACS installation with the GROMACS Wizard in SAMSON, follow these steps:

  1. Click the Settings button at the top of the GROMACS Wizard UI.
  2. Enable the option Use a different GROMACS version.
  3. Set two paths:
    • The path to your gmx executable (or gmx.exe on Windows).
    • The path to your force fields directory (e.g., $HOME/gromacs/share/top/).

Custom GROMACS path

The wizard will validate the selected binary and display its version. If the binary cannot be recognized, it will simply mark it as “invalid,” so you’ll know right away if something needs fixing.

Pro tip: Centralize your GROMACS builds

If you work across multiple projects or teams, consider maintaining a central GROMACS installation per version, with separate force field folders. This way, different users and pipelines can easily point to a shared, validated setup—reducing debugging time when reproducing prior simulations.

To learn more about customizing your GROMACS settings in SAMSON, visit the full documentation: 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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