When working with coarse-grained (CG) molecular simulations, many modelers run into unexpected behavior during solvation—particularly with Martini models. This blog post dives into why solvent setup in the GROMACS Wizard in SAMSON requires an extra step, and how skipping it can lead to inaccurate simulations.
In all-atom models, van der Waals (vdW) radii between atoms are well-defined and used to avoid steric clashes. But that’s not the case with CG models, especially MARTINI water beads where one particle represents multiple molecules. Here’s the issue: by default, GROMACS uses a vdW distance of 0.105 nm during solvation, which is tuned for atomistic systems. For CG systems, this default distance places solvent molecules too close together, potentially causing overlapping beads and incorrect densities.
Adjusting the van der Waals Distance in SAMSON
Fortunately, GROMACS Wizard in SAMSON allows you to easily modify this parameter during solvent setup. Here’s how to do it during Step 1: Prepare.
- Ensure you’ve loaded your system files (e.g.,
*_CG.pdb,*_CG.top) generated with Martinize2. - In the Prepare tab, check Add solvent and click the gear icon next to it.
- In the options pop-up, change the default van der Waals distance to a larger value. 0.21 nm is a good starting point.
This small tweak will space out solvent beads more appropriately for CG systems and help maintain realistic solvent density. Here’s how it looks:
When You Might Forget This Step
It’s an easy step to overlook, especially if you’re used to running all-atom simulations where GROMACS handles most defaults reliably. But CG simulations require some mindful adjustments. Solvent overlap, density artifacts, or buried hydrophilic beads can all stem from neglecting this subtle, but critical detail.
Custom Solvent Models?
If you’re using a custom CG force field or developing your own water models, you can also provide a different solvent model file entirely. The GROMACS Wizard lets you do this too. You can learn more in the section on Using a custom solvent model.
Bottom Line
If your CG simulations seem unstable or unrealistic, double-check how you’re solvating. Switching the vdW distance for solvation is one of those overlooked details that can save you countless debugging hours later.
Learn more in the full documentation page: 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.