Why and How to Use Your Own GROMACS Version in SAMSON

Molecular modelers working with GROMACS often rely on specific versions of the simulation software, either for reproducibility or to take advantage of local custom builds. However, many tools that simplify the setup of molecular dynamics simulations don’t make it easy to switch GROMACS versions. If you’re using SAMSON and the GROMACS Wizard extension, there’s good news: this flexibility is built-in, and setting it up is more straightforward than you might expect.

By default, GROMACS Wizard comes with a bundled version of GROMACS. But you might prefer to use a different version—perhaps you already compiled GROMACS on your machine with GPU acceleration, or you need an earlier release for consistency with published results.

When You Might Want to Use a Custom Version

Here are some common reasons users choose their own GROMACS version instead of the one provided:

  • You compiled GROMACS with specific performance optimizations or libraries (e.g., GPU, MPI).
  • You are reproducing simulations that were originally run with a specific GROMACS release.
  • Your system administrator installed GROMACS system-wide and it’s already configured.

Setting It Up in SAMSON

To use your own GROMACS version in SAMSON’s GROMACS Wizard:

  1. Open the GROMACS Wizard in SAMSON, then click the Settings button at the top.
  2. In the Settings panel, turn on the option Use a different GROMACS version.
  3. Provide the path to your local GROMACS executable (this is typically gmx on Linux/macOS or gmx.exe on Windows).
  4. The Wizard will validate the version and display it (you’ll get a warning if the path is invalid).
  5. Provide the path to your force fields directory. On Linux/macOS, this is often in $HOME/gromacs/share/top/.

Custom GROMACS path

These steps allow you to keep the familiar SAMSON interface while relying on your existing GROMACS installation. You can now run local jobs that use your own customized binaries and force fields, without requiring additional scripts or configurations.

Some Tips When Using a Custom Version

  • Make sure that the GROMACS version you’re using is compatible with your input files, especially if you’ve downloaded them from external sources.
  • If the version field shows “invalid,” double-check the filename, path, and whether the executable runs independently.
  • Use the opportunity to match the forcefield directory carefully. A mismatch here can produce errors that are otherwise hard to debug later.

With this flexibility, you don’t have to give up your workflow optimizations just to benefit from SAMSON’s graphical tools. This small configuration step can help you ensure consistency and performance across projects.

To learn more about this feature and other GROMACS Wizard settings, visit the official documentation page.

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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