Easily Switch to Your Custom GROMACS Version in SAMSON’s GROMACS Wizard.

As a molecular modeler, you may often face scenarios where the default setup of a tool doesn’t align precisely with your preferences or the requirements of your research system. If you’re using SAMSON’s GROMACS Wizard, this might happen when the built-in version of GROMACS doesn’t match the one you need. Whether it’s for ensuring reproducibility, leveraging specific algorithms, or adhering to established lab protocols, using your own custom GROMACS version can make all the difference. Here’s how SAMSON’s GROMACS Wizard empowers you to easily set up and use your own preferred version of GROMACS.

Why Use a Custom GROMACS Version?

The GROMACS Wizard in SAMSON comes pre-packaged with one of the latest GROMACS versions. While this ensures users have access to up-to-date functionalities out of the box, you may have compelling reasons to use your specific locally installed GROMACS version:

  • You value reproducibility in your simulations and want to use the exact GROMACS version employed in prior studies.
  • Your research relies on features or algorithms available only in older or custom-compiled versions of GROMACS.
  • You prefer to integrate the GROMACS executable already installed and optimized on your local system.

How to Configure Your Custom GROMACS Version

Configuring a custom version in GROMACS Wizard is straightforward. Start by clicking on the Settings button at the top of the GROMACS Wizard interface.

Open settings

In the Settings window, you’ll notice the version of the pre-packaged GROMACS setup. To switch to your local version:

  1. Check the Use a different GROMACS version option.
  2. Provide the path to the GROMACS executable (e.g., gmx.exe for Windows or gmx on Linux/macOS). Use the browse button browse to locate the executable easily. If the executable is recognized, the version will be displayed. If not, you’ll see an invalid message.
  3. Add the path to the folder containing your force field directories (e.g., $HOME/gromacs/share/top/ on Linux/macOS).

The interface even provides feedback by showing which version of GROMACS has been selected, giving you confidence that the setup is correctly aligned.

Custom GROMACS path

Key Benefits of This Flexibility

  • Reproducibility: Easily configure legacy GROMACS versions to match previously published simulation environments.
  • Familiarity: Use a GROMACS version you are most comfortable with, minimizing the learning curve.
  • System-specific Optimization: Utilize GROMACS versions compiled and fine-tuned for your hardware configuration.

This feature enables you to make the most of your local resources while seamlessly integrating with SAMSON’s powerful molecular design tools.

Getting Started

Once your configuration is complete, you can proceed to run your local simulations without any hassle. The GROMACS Wizard allows you to switch effortlessly between the provided GROMACS setup and your custom version, ensuring flexibility and precision in your workflow.

To dive deeper into this feature, including additional performance parameters and advanced use cases, visit the GROMACS Wizard documentation.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Ready to get started? Download SAMSON now at https://www.samson-connect.net.

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