When preparing a coarse-grained (CG) system for molecular dynamics simulations, one of the most overlooked yet essential steps is setting the correct force field. In SAMSON’s GROMACS Wizard, the careful selection of the right coarse-grained force field can make or break your entire simulation workflow. This post walks through common mistakes and how to avoid them — whether you’re using the default martini_v.3.0.0 force field or your own custom setup.
Why the Force Field Choice Matters
Force fields define how particles interact — including bonded and non-bonded terms — making them central to the accuracy of any molecular system simulation. Unlike all-atom models, coarse-grained models represent molecules with fewer particles (beads), and the interactions are specifically tuned for these grouping strategies.
Failing to set the proper CG force field when preparing your system can lead to incorrect solvation behavior, instability during minimization, or unrealistic results in dynamics simulations. Fortunately, GROMACS Wizard helps automate several parts of this, but there are some details you shouldn’t miss.
Default Help: MARTINI v.3.0.0 Auto-Detection
If you’re using a CG model generated by Martinize2, SAMSON’s GROMACS Wizard automatically detects this and sets the force field to martini_v.3.0.0.
This saves time and prevents mismatched parameter files. Still, it’s worth verifying that the force field dropdown lists martini_v.3.0.0 after loading your system.
What If You’re Using a Custom Coarse-Grained Model?
Let’s say you’re not using MARTINI or you generated a CG model elsewhere. In that case, you’ll need to manually set the appropriate force field in GROMACS Wizard. This involves:
- Importing your custom parameter files (e.g., .itp, .top).
- Ensuring the file paths and defines in your topology are consistent.
- Selecting the correct force field from the dropdown or configuring a custom one through the custom force field interface.
GROMACS Wizard maintains compatibility, but since solvent and ion behavior may vary by force field, it is essential to check corresponding solvent definitions as well.
Interaction with Solvent Models and Other Parameters
Force field selection in the CG world isn’t just about bond strengths. Because the MARTINI water model uses one CG bead to represent four water molecules, solvation parameters — such as the van der Waals radius — must also be suitably modified. For MARTINI, for example, SAMSON suggests increasing the default van der Waals distance to around 0.21 nm.
This protects the integrity of the packing and solute-solvent interactions, which are critical for realistic equilibration. GROMACS Wizard allows editing these distances through a gear icon next to the Add solvent option, providing a simple UI for otherwise command-line-heavy edits.
Conclusion
Choosing the right force field at the preparation stage prevents a host of downstream issues. SAMSON’s GROMACS Wizard helps streamline this decision, especially for users of Martinize2 and MARTINI v.3.0.0, but the responsibility still lies with the modeler to ensure consistency between the molecular system and force parameters.
Before hitting the “Prepare” button, double-check your force field selection and solvent compatibility. Your future self — and your CPU cycles — will thank you.
To learn more, visit the full documentation page here: https://documentation.samson-connect.net/tutorials/gromacs-wizard/coarse-grained-systems/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.