Running your own GROMACS version in SAMSON without breaking a sweat

Running molecular dynamics simulations with GROMACS? If you’ve ever needed to use a specific version of GROMACS (perhaps for reproducibility, GPU support, or compatibility with certain force fields), you know how frustrating it can be to tie everything together smoothly—especially when working with graphical interfaces.

The GROMACS Wizard in SAMSON now makes it easy to plug in your own GROMACS version and use local resources effectively—no command-line stress required. Let’s walk through how and why you might want to do this.

Why use a custom GROMACS version?

While SAMSON ships with a recent version of GROMACS, you might prefer to use your own local build to:

  • Ensure reproducibility (especially if your lab standardizes on a specific version).
  • Take advantage of GPU acceleration or specific compilation flags.
  • Use specialized patches or dependencies in custom environments, like HPC clusters.

The good news? No code editing or terminal magic needed.

How to configure a custom GROMACS setup in SAMSON

1. Inside the GROMACS Wizard interface in SAMSON, click the Settings button at the top right:

Open settings

2. In the Settings panel, check “Use a different GROMACS version”.

3. You’ll be asked to provide two things:

  1. The path to your local GROMACS executable – This is gmx on Linux/macOS or gmx.exe on Windows. Click the folder icon to browse and select the right file. SAMSON will verify the version you choose.
  2. The path to your force field folder – This should point to the directory where your .ff force fields are stored. Typical paths might look like $HOME/gromacs/share/top/.

Custom GROMACS path

That’s it. From now on, whenever you launch a local simulation from GROMACS Wizard, it will use your GROMACS installation—not the bundled one.

When this matters most

This workflow is especially useful if:

  • You’ve installed a GROMACS version optimized for your CPU/GPU combo.
  • You’re part of a research team that uses a containerized (e.g., Singularity or Docker) GROMACS build with unique configurations.
  • You’re submitting results for publication and need to show simulations run with identical binaries and parameters.

It’s also a great way to avoid modifying your primary GROMACS installation when experimenting with different settings or system setups in SAMSON.

Learn more in the official GROMACS Wizard documentation.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.

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