When preparing a coarse-grained (CG) molecular system, especially using the MARTINI force field, it’s easy to overlook a small yet critical detail that can impact your entire simulation: the default van der Waals (vdW) distance used during solvation.
This post is for molecular modelers who use GROMACS Wizard in SAMSON to prepare CG systems. If you’ve encountered issues like unrealistic water densities or overlapping beads during the solvation of your CG model, this will likely sound familiar. 😓
What’s the problem?
GROMACS, by default, uses a van der Waals distance of 0.105 nm when placing solvent molecules. This value works fine for all-atom simulations, but it’s too tight for coarse-grained models, especially with the MARTINI force field, where a single water bead can represent four actual water molecules. If you don’t adjust this vdW distance, water beads might be placed too close to each other or to the solute, resulting in overlaps and poor system stability.
The solution in SAMSON’s GROMACS Wizard
SAMSON’s GROMACS Wizard helps by allowing users to customize the solvation settings—an essential step that can save you time troubleshooting later on. Here’s how to do it:
- Once you’ve loaded your CG system and confirmed that MARTINI v.3.0.0 is selected as the force field, check the Add solvent option.
- Click the small gear icon
to access solvation options. - In the pop-up dialog, locate the van der Waals distance setting. Increase it to 0.21 nm. This value reduces the likelihood of overlaps and ensures a more realistic density for MARTINI water beads.
- You can leave other solvation parameters at their default values, or optionally provide a custom solvent model.
Why does this matter?
A proper solvation setup ensures that your simulation starts on the right foot. Overlapping solvent molecules at the beginning might cause energy minimization steps to fail, or result in unstable dynamics during equilibration. Taking a few seconds to tweak this parameter allows your system to avoid unnecessary problems down the line.
Troubleshooting tip
If you’ve already run into trouble and suspect vdW clashes are to blame, try visualizing your initial solvated model in SAMSON. The visualization tools will make any overlaps or dense packing painfully obvious.
More options if you need them
GROMACS Wizard also supports using custom CG solvent models. So if you’re relying on a different setup (or perhaps developing your own model), you can plug it right in. See the dedicated documentation section on custom solvents for more information.
To learn more about setting up coarse-grained systems with SAMSON’s GROMACS Wizard, visit the full tutorial here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.