When setting up coarse-grained (CG) molecular dynamics simulations, solvation may seem like a straightforward checkbox. However, if you’re using the MARTINI v.3.0.0 force field with coarse-grained beads and GROMACS, there’s a subtle — but impactful — parameter you should not overlook: the default van der Waals (vdW) distance.
By default, GROMACS does not define vdW distances for CG beads. During solvation, it resorts to a generic value of 0.105 nm, which is perfectly reasonable for all-atom simulations — but for CG models like MARTINI, it’s often too small. One Martini water bead represents four water molecules, so packing them too closely can result in unphysical overlaps and poor solvent density. This can negatively affect energy minimization and the stability of your simulation later on.
Here’s how you can address this issue when using the GROMACS Wizard in SAMSON to prepare your system:
Setting the Right Solvent Options
- Enable the Add solvent option after loading your CG system.
- Click the gear icon next to Add solvent to open the solvent options:
- In the pop-up window, increase the default vdW distance to a value like 0.21 nm. This helps avoid overlapping beads and creates a more realistic solvent distribution.
You can leave all other parameters at their default values unless you have a reason to modify them.
Why It Matters
This adjustment might seem small, but it’s essential if you want to avoid the following:
- Atom clashes during energy minimization
- Unrealistic solvent density, which may require additional equilibration time
- Simulations crashing or becoming unstable early on during production runs
This simple step can save time and avoid lengthy debugging. Many users unfamiliar with coarse-grained modeling assume default parameters apply equally — but as this example shows, CG models come with their own quirks.
Want more control? The GROMACS Wizard in SAMSON even allows you to use your own custom solvent model. But if you’re working with MARTINI, this vdW tweak is often all it takes to stabilize your setup.
To learn more about system preparation for coarse-grained models and how to proceed with solvation, ion addition, and box setup, check the full guide here:
https://documentation.samson-connect.net/tutorials/gromacs-wizard/coarse-grained-systems/
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.