When Reproducibility Matters: Running GROMACS Simulations with Your Preferred Version

As a molecular modeler, you might have encountered the following situation: you’re trying to reproduce simulations from a paper, or continue a project started on another machine. But your local GROMACS version doesn’t quite match the one previously used. Differences between GROMACS versions, even minor ones, can sometimes lead to changes in behavior, performance, or compatibility with certain force fields. This makes reproducibility a challenge — and that’s where the GROMACS Wizard in SAMSON can help.

The GROMACS Wizard integrates GROMACS directly into the SAMSON platform and allows you to configure advanced simulation parameters in just a few clicks. One particularly useful feature: the ability to use a custom version of GROMACS installed on your machine.

Why Use a Custom GROMACS Version?

Although the GROMACS Wizard ships with a recent version of GROMACS, you might want to run simulations with a specific version for compatibility or reproducibility. For example:

  • You’re replicating results published with an older GROMACS version
  • Your computation cluster has a pre-installed version
  • You’ve compiled GROMACS with specific performance optimizations

How to Set It Up in SAMSON

Setting up your own GROMACS version is simple:

  1. Click on the Settings button in the GROMACS Wizard toolbar.
  2. Enable the option “Use a different GROMACS version”.
  3. Browse to select your gmx executable (gmx.exe on Windows).
  4. Specify the directory containing your forcefield.ff folders. On Linux/macOS, this might be $HOME/gromacs/share/top/.

This will allow GROMACS Wizard to verify and use your specified version, and display whether the executable is valid.

Custom GROMACS path

Helpful Tips

🔹 Try keeping your GROMACS installation paths consistent across machines or clusters if reproducibility matters.

🔹 If you installed GROMACS with cmake, make sure you’re pointing to the correct binaries — sometimes environments need to be sourced first (e.g., using source GMXRC).

🔹 Keep in mind that if your version is too old or too new, some features of the GROMACS Wizard might not work as expected. Compatibility is generally best with GROMACS versions 5.0 and above.

Maintaining Flexibility

This feature especially shines when working in collaborative environments or education — where students can run the same simulations, with the same settings, under identical conditions using the same GROMACS version. It’s also useful when exploring performance differences between versions compiled with distinct hardware optimizations (e.g., AVX-512 or CUDA).

To learn more, visit the full documentation: GROMACS Wizard settings – SAMSON Documentation.

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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