Using Your Own GROMACS Version in SAMSON: When and Why It Matters

Many molecular modelers rely on GROMACS for molecular dynamics simulations, and SAMSON’s GROMACS Wizard provides a user-friendly way to perform these simulations locally or in the cloud. But did you know that SAMSON also allows you to use your own custom GROMACS installation?

This is an important feature with real benefits—especially if your research workflow depends on specific GROMACS versions for reproducibility, or if you’ve already optimized a local GROMACS setup.

Why use a custom GROMACS version?

If you’re working toward publication or comparing results across platforms, sticking with a known GROMACS version is often essential. Different versions may have slight variations in force field handling or algorithm implementations. Reproducibility matters—and SAMSON helps you with that.

How to set it up

Selecting your own installed version of GROMACS in SAMSON is straightforward. Here’s how:

  1. Open the GROMACS Wizard in SAMSON and click the Settings button.

    Open settings
  2. In the Settings panel, check the box labeled Use a different GROMACS version.
  3. Provide two paths:

    • The path to your GROMACS executable (e.g., gmx or gmx.exe).
    • The path to your force fields folder containing forcefield.ff directories (e.g., $HOME/gromacs/share/top/).

    Custom GROMACS path

SAMSON will validate your selected GROMACS executable. If it’s compatible, the version will be displayed. Otherwise, it will show as “invalid.” This quick feedback helps verify that your setup is functional.

When is this especially useful?

Using a local version of GROMACS is helpful when:

  • Your institution distributes a specific GROMACS build optimized for your hardware.
  • You need your results to match previously published simulations using an older version.
  • You’re debugging or cross-testing with particular features (e.g., custom-modified source code).

Keep your workflow adaptable

This flexibility makes SAMSON a useful front-end for anyone doing serious molecular modeling—letting you benefit from a GUI while maintaining close control over your environment. Integrating your local GROMACS setup with SAMSON is also useful for teaching settings where students share the same version across OSes.

To learn more about configuration options, including custom performance settings, check the full documentation page: GROMACS Wizard Settings in SAMSON.

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

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