Coarse-grained (CG) molecular dynamics is a common approach to simulate large biomolecular systems with reduced computational cost. The GROMACS Wizard in the SAMSON platform provides an intuitive interface to set up such systems, including generating periodic boxes, adding solvent, and preparing for simulation. However, one easily overlooked step can cause significant issues: improperly spaced solvent molecules.
Let’s look more closely at this common scenario: you’re trying to solvate a CG system—perhaps generated with Martinize2 using the MARTINI v.3.0.0 force field—but your run fails due to steric clashes. The reason? Default van der Waals (vdW) radii in GROMACS are too small for CG models without explicit vdW parameters. Here’s how to avoid that.
The Issue: Too-Tight Solvent Packing
In CG models like those using MARTINI, water beads represent multiple real molecules (usually 4 waters per bead). GROMACS, by default, assumes a vdW distance of 0.105 nm for undefined atom types. For CG systems, this can result in solvent packing that’s physically unrealistic—leading to overlaps, incorrect densities, and simulation errors.
Solution: When using SAMSON’s GROMACS Wizard to solvate a CG system, you need to manually increase the default vdW exclusion distance before solvent is added.
How to Do It in GROMACS Wizard
After specifying your system inputs, and ensuring the MARTINI 3.0.0 force field is selected, make sure to:
- Enable the Add solvent checkbox in the Prepare tab.
- Click the gear icon next to this checkbox to open advanced solvent settings:
- Find the van der Waals (vdW) distance and change it from the default
0.105 nmto at least0.21 nm.
This simple change ensures that solvent beads are spaced realistically around CG solute structures, avoiding density artifacts or atomic overlaps.
Why It Matters
Skipping this step can cause unnecessary simulation failures at the equilibration or minimization stages. Worse, you might not spot the error until much later in your pipeline.
By adjusting just one parameter early in system preparation, you can save hours of troubleshooting. This is especially important if you’re setting up batch simulations or using automation tools with coarse-grained frameworks.
For users working with custom solvent models (e.g., for polarizable beads or other force fields), remember to adjust this setting accordingly. GROMACS Wizard also allows you to define your own solvent models if needed.
To learn more about this and other important system preparation steps, including defining the box, adding ions, and using position restraints, check the full documentation 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 from https://www.samson-connect.net.