Using Your Own GROMACS in SAMSON Wizard: Why and How

Many molecular modelers rely on the GROMACS engine for performing complex molecular dynamics simulations. While using the default versions bundled with visualization platforms is convenient, there are valid reasons to switch to a custom GROMACS version for local jobs. Whether for reproducibility, legacy compatibility, or specific GPU optimizations, having the freedom to run your own compiled version of GROMACS can be essential. Fortunately, the GROMACS Wizard in SAMSON makes this easy.

Let’s take a closer look at when — and how — to use your own GROMACS installation within the SAMSON environment.

Why use a custom GROMACS version?

There are a few common motivations behind this:

  • Reproducibility: If a previous simulation was run using GROMACS 2019.3, it’s often prudent to use the same version when revisiting or building upon that simulation.
  • Hardware optimization: You may have compiled GROMACS with CUDA support for GPU acceleration, or tailored compilation flags specific to your system architecture.
  • Consistency across tools: Some users work across several environments or clusters. By aligning versions, you reduce compatibility issues.

How to activate your local GROMACS installation

GROMACS Wizard normally uses a bundled version of GROMACS. To use your local version instead:

  1. In the GROMACS Wizard interface, click the Settings button at the top.
  2. In the settings panel, check the Use a different GROMACS version option.
  3. Provide two paths:
    • The path to the gmx executable (or gmx.exe on Windows). This can be selected via the folder browse button: browse
    • The path to your local force fields directory. For example, $HOME/gromacs/share/top/ on Linux or macOS.

If the provided executable is valid, the version will be displayed next to it. If not, “invalid” will be shown — make sure your executable is accessible and properly built.

Custom GROMACS path

Force Fields Directory

GROMACS Wizard uses this directory to find available force fields (i.e. folders like amber99sb-ildn.ff). Make sure the path you provide contains the right structure — otherwise your simulations may fail at the preparation stage.

Quick tips

  • If you manage multiple GROMACS installations, consider creating a small bash script to toggle environment variables and symlinks as needed.
  • If performance matters, don’t forget to install and compile GROMACS with GPU support if you have a compatible system.

Configuring GROMACS Wizard to use your own version takes just a minute, and it gives you greater flexibility and control over your simulations.

To learn more, visit the full documentation page here: https://documentation.samson-connect.net/tutorials/gromacs-wizard/settings/

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download them at https://www.samson-connect.net.

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