When working on molecular dynamics simulations with GROMACS, ensuring reproducibility and compatibility with previous publications or validated workflows is often essential. But what if your workflow relies on a specific version of GROMACS that’s not exactly the one bundled within another platform?
This is a common concern among molecular modelers, especially when migrating to new platforms—or working in collaborative settings where researchers rely on a specific toolchain. Fortunately, SAMSON’s GROMACS Wizard offers a flexible solution: it allows you to use a custom version of GROMACS for your local jobs.
Why Use Your Own Version of GROMACS?
There are several reasons for doing so:
- You have a validated workflow tied to a specific GROMACS version (for example, 2019.6).
- Your system administrator maintains a centrally installed version optimized for your local HPC system.
- You’re investigating reproducibility and want to match your earlier runs byte-for-byte.
SAMSON’s GROMACS Wizard respects this need for flexibility by allowing you to define your own GROMACS path and forcefield directory.
How to Set It Up in SAMSON
From inside the GROMACS Wizard interface in SAMSON, click the Settings button at the top of the Wizard panel:
In the Settings pane, check the box labeled “Use a different GROMACS version”.
- Executable Path: Click the folder icon to browse for your GROMACS executable (e.g.,
gmxorgmx.exe). Once selected, SAMSON automatically tries to detect and display the version. - Forcefield Folder: Provide the path to the folder that contains your
forcefield.ffdirectories (typically something like$HOME/gromacs/share/top/).
If the executable is valid, the Wizard will accept it and all your local jobs will now use your preferred GROMACS build. If it’s invalid (for example, pointing to the wrong binary or an incomplete installation), a warning will inform you so that you can fix it.
Tips for a Smooth Setup
- Make sure your selected GROMACS version works from the terminal before linking it to SAMSON.
- Check that your forcefield directory contains all necessary files (especially if using custom or legacy forcefields).
- You can always return to using SAMSON’s bundled version by unchecking the “Use a different GROMACS version” option.
What About Cloud Jobs?
It’s important to note that this configuration only affects local computations. Cloud jobs will continue using the server-side default GROMACS version, ensuring consistency across different users’ jobs in the cloud environment.
This feature offers a valuable bridge between the convenience of an integrative platform and the control that many advanced users need for fine-tuned simulations.
To learn more about running your own GROMACS version or enabling advanced performance parameters, visit the official documentation page: GROMACS Wizard Settings — SAMSON Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.