Choosing the right force field is a recurring concern for molecular modelers, especially when dealing with non-standard molecules or specific biochemical conditions. While GROMACS provides several standard force fields, sometimes they just don’t cut it—especially when you need to simulate systems with ligands or molecules not covered by the defaults.
This is where the GROMACS Wizard in SAMSON offers a practical solution: you can add your own custom force fields and use them seamlessly during the simulation setup process.
Why use custom force fields?
Standard force fields like OPLS-AA or AMBER are suitable for many applications, but custom molecules such as novel ligands, cofactors, or synthetic compounds may not be fully parameterized in these sets. If you’ve obtained .itp files from the ATB or CGenFF server, you’ll likely need to load them together with the matching force field to perform reliable simulations.
How to integrate a custom force field in SAMSON’s GROMACS Wizard
1️⃣ In the Model section of the GROMACS Wizard, click on the Add button next to the force field dropdown. A dialog appears, allowing you to provide the path to your custom force field directory.
2️⃣ Once added, your force field appears in the list so you can select it just like a default one. SAMSON even validates the files to ensure compatibility with GROMACS.
3️⃣ To remove previously added custom force fields, just click the Remove button (also shown below). Note that this only affects custom fields—you’ll still have access to the built-in ones.
Pairing your custom force field with additional topology files
If your molecule is not described in the force field, you’ll also need to load its topology. SAMSON makes this straightforward:
- Simply import your
.itpfiles via the interface. - Make sure they were created using the same force field you’ve just added.
You can get these topology files from services such as:
- ATB Server – useful for GROMOS-compatible topologies.
- CGenFF server – for CHARMM-based systems.
Tip: Be force-field consistent
⚠️ It’s crucial that your topology files and your custom force field match. Mismatches can lead to failed preparations or incorrect simulations. If you generate topologies using ATB, make sure to download the corresponding force field (e.g., gromos54a7_atb).
Final thoughts
Whether you’re simulating small ligands, novel cofactors, or other complex molecules, customizing your force field gives you the flexibility needed for accurate molecular simulations. SAMSON’s GROMACS Wizard lowers the barrier to using custom setups by providing a clear interface for force field and topology integration—no manual edits or CLI gymnastics needed.
Learn more about the preparation phase, including force fields and beyond, in the full GROMACS Wizard preparation tutorial.
SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at https://www.samson-connect.net.