Many researchers working with molecular dynamics simulations rely on GROMACS for its performance and flexibility. But one common challenge emerges: how do you integrate a specific version of GROMACS — perhaps compiled with custom flags or needed for reproducibility — into a general-purpose GUI like SAMSON?
By default, the GROMACS Wizard in SAMSON comes with a built-in, recent version of GROMACS. While this is convenient, certain workflows or publication requirements might demand more control. Whether you want to stick with a previously validated version or leverage special performance options enabled in your local build, SAMSON makes it possible to use your own GROMACS installation with just a few clicks.
Why Use a Custom GROMACS Version?
- Reproducibility: Scientific reproducibility sometimes depends on using identical software versions, including exact GROMACS builds configured with specific options.
- System Compatibility: If your local system already has GROMACS compiled with hardware-specific optimizations (e.g., AVX-512), using that version may lead to better performance than a generalized build.
- Pre-configured Force Fields: You may have force fields organized in your local directories that fit your workflow better than the default setup.
Setting It Up in SAMSON
To use your own installed version of GROMACS inside SAMSON’s GROMACS Wizard:
- Open the GROMACS Wizard in SAMSON.
- Click the Settings button at the top of the interface.
Under the version section, check the box labeled Use a different GROMACS version. This reveals two fields you need to fill:
- A path to your GROMACS executable (typically
gmxorgmx.exe). - A path to your local force field folder (e.g.,
$HOME/gromacs/share/top/).
If done correctly, SAMSON will recognize the version information from your executable. If it’s not recognized, the field will display “invalid” — double check your file paths or GROMACS build in that case.
When Would This Be Especially Helpful?
Suppose you’re submitting a paper and need to rerun simulations using GROMACS 2022.4, because that’s what was used in your early exploratory runs. Or imagine your computing cluster runs its own optimized build. Rather than conforming to the built-in version, you can now bring your workflow into SAMSON, aligning your GUI-based setup with your terminal-based runs seamlessly.
Force Fields and Directory Structure
Don’t forget that GROMACS expects a folder containing forcefield.ff directories. Whether you’re using GROMOS, AMBER, or OPLS force fields, ensure your path points to the location where those subfolders live. On Linux and macOS, it’s commonly in $HOME/gromacs/share/top. On Windows, it varies depending on your installation.
Final Thoughts
Using your own GROMACS version in SAMSON is straightforward, and it offers a lot more control over your molecular dynamics setups. It’s especially useful when hardware-specific builds or version consistency are part of your research requirements.
Learn more in the official GROMACS Wizard settings documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.