When You Need Your Own GROMACS: Using Custom Versions in GROMACS Wizard

Reproducibility is a core concern in molecular modeling. Whether you’re publishing results, working with legacy systems, or using specific patches, there are situations where the default GROMACS installation — even the latest one — just won’t do. Fortunately, the GROMACS Wizard in SAMSON supports running simulations with a custom version of GROMACS that’s already installed on your local system.

So, when would you want to do this?

  • 🔄 To reproduce results exactly as described in a publication based on a specific GROMACS version.
  • 🎓 To work on a course or project that mandates a particular set of parameters or force fields available only in older versions.
  • ⚙️ Because you’ve compiled a GROMACS version with custom patches or performance settings.

Whatever the reason, GROMACS Wizard lets you easily switch to your desired version. Here’s how it works:

Accessing GROMACS Wizard Settings

First, click the Settings button in the top-right corner of the GROMACS Wizard interface.

Open settings

Selecting a Custom Executable

Under settings, you’ll see the version of the GROMACS package that ships with SAMSON’s GROMACS Wizard. To use a different one, check the option Use a different GROMACS version. You’ll then need to enter two paths:

  1. The path to your custom GROMACS executable: Usually gmx on Linux or macOS, or gmx.exe on Windows. Use the file browser button for easier navigation.
  2. The path to your forcefields directory: This is where GROMACS stores its .ff folders, e.g., $HOME/gromacs/share/top/.

Custom GROMACS path

Once both paths are entered, GROMACS Wizard will validate the inputs. If the wizard cannot recognize the version, it will mark the executable as “invalid” — a useful verification step to catch errors early.

Important Considerations

  • Make sure your GROMACS version is compatible with the force fields you’re using.
  • The executable must be accessible from the system you’re running SAMSON on — remote execution paths aren’t supported here.
  • Note that using a custom version will only apply to local jobs. Cloud simulations through SAMSON use the default version included with the extension.

This flexibility allows users to integrate SAMSON’s ease of use with the custom setups often required in real-world research workflows. Many users working in academic environments or regulated industries will appreciate being able to align their simulations with existing GROMACS setups.

To learn more about related performance settings and advanced behavior, check the full documentation here: GROMACS Wizard Settings.

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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