Running Simulations with Your Own GROMACS Version in SAMSON

Molecular modelers often face a critical challenge when it comes to reproducibility and performance of molecular dynamics simulations. If your workflows rely on a customized or system-specific build of GROMACS—for example to support consistent academic publishing or ensure compatibility with other system-level software—you might have encountered tools that do not allow integration with your local GROMACS installation.

The GROMACS Wizard included in SAMSON addresses this issue by allowing you to plug in your own version of GROMACS. This offers a smoother, customizable environment for running molecular dynamics simulations while retaining the intuitive interface of the SAMSON platform.

Why use a custom GROMACS version?

There are multiple reasons you might want to do this:

  • You have a specific version of GROMACS validated for your research group or project.
  • You rely on features or patches that are not available in the default GROMACS build bundled with SAMSON.
  • You need to use performance-optimized builds (e.g. with GPU or MPI support) fine-tuned for your local cluster or workstation.

How to set it up

Integration with your local GROMACS version is done through the Settings panel of the GROMACS Wizard:

Open settings

In the Settings panel, you can check the box labeled Use a different GROMACS version. This opens up two fields you need to fill:

  1. Path to executable: Provide the full path to your local gmx or gmx.exe executable. SAMSON will validate the executable and show a warning if it isn’t recognized.
  2. Path to force fields folder: This is where your force fields like amber99sb-ildn.ff or gromos53a6.ff live. For typical installations on Linux or macOS, this would be something like $HOME/gromacs/share/top/.

Custom GROMACS path

Common pitfalls

Here are a few things to watch out for:

  • Make sure your local GROMACS build is complete and compiled with the same naming conventions.
  • If the executable isn’t validated (shown as “invalid”), double-check the file path and permissions.
  • Force field directory should include actual subfolders ending with .ff such as amber99sb-ildn.ff.

Benefits during collaboration and publication

When multiple researchers use different systems but the same local installation of GROMACS, enabling this feature ensures consistent simulation behavior. It also removes ambiguity when submitting your system configuration for peer review or depositing simulation datasets for reproducibility.

To summarize, if you’ve ever struggled with integrating your existing simulation setup into graphical platforms, the GROMACS Wizard in SAMSON provides a practical, user-friendly way to run simulations with your own tools—without sacrificing interface simplicity.

📖 Learn more in the original documentation.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.

Comments are closed.