If you’re working with coarse-grained (CG) systems using the MARTINI force field, you’ve probably encountered unexpected issues when solvating your system. Molecules may appear too close to each other, or your system might behave strangely during simulation setup. A common culprit? Incorrect van der Waals (vdW) distance settings for solvent placement. In this blog post, we’ll explore why solvating CG systems requires special care and how the GROMACS Wizard in SAMSON can help you easily address it.
Why van der Waals Distance Matters
In atomistic simulations, GROMACS uses defined vdW parameters to prevent atomic overlaps when inserting solvent molecules. However, in CG systems — specifically those using the MARTINI force field — vdW parameters aren’t defined in the same way. Each water bead in MARTINI represents four water molecules, making them significantly larger than individual water molecules in atomistic models.
By default, GROMACS uses a fallback vdW distance of 0.105 nm. While this may be sufficient for atomistic systems, it is too small for CG beads. The result? Water beads may be placed too close to solute molecules, increasing the risk of physical clashes and unrealistic densities.
The Solution: Adjusting Solvent Options in GROMACS Wizard
The GROMACS Wizard Extension in SAMSON makes solvating CG systems easier by allowing you to customize solvent insertion parameters directly from the GUI. Here’s a simple step-by-step guide:
- After loading your CG system in the Prepare tab, check the Add solvent option.
- Next to it, click on the gear icon to access solvent insertion settings:
- In the popup window, increase the default van der Waals distance from
0.105 nmto a more appropriate value for CG models — for example,0.21 nm.
Increasing the vdW distance ensures water beads aren’t placed too close to solute atoms, which helps achieve proper solvent density and reduces clashes that could cause crashes or artifacts during energy minimization.
What If You’re Using a Custom Solvent?
GROMACS Wizard is also flexible enough to let you provide a different CG solvent model. This can be helpful if you’re working with a specialized system or testing alternative parameterizations. You can read more on using custom solvents in the GROMACS Wizard documentation.
Summary
Properly solvating CG systems is more than just clicking a checkbox — it requires adjusting the vdW insertion distance to values suitable for coarse-grained beads. Thanks to the intuitive interface in SAMSON’s GROMACS Wizard Extension, this can be done quickly and reliably with just a few clicks.
To learn more, visit the full documentation page: GROMACS Wizard – Coarse-grained systems.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON here.