Setting up coarse-grained (CG) molecular simulations can be rewarding—but also tricky. One of the most common setup issues for newcomers and experienced users alike is related to solvent behavior. CG models, especially those using the popular MARTINI force field, coarse-grain four water molecules into a single bead. This simplification is great for simulation speed, but it requires some thoughtful preparation choices—particularly when solvating your system.
In this post, we shed light on an often overlooked yet essential step when working with coarse-grained systems in SAMSON’s GROMACS Wizard: adjusting the van der Waals (vdW) distance during solvation to avoid overlapping solvent beads, unstable simulations, or unwanted density artifacts. 🧪
What’s the problem?
By default, GROMACS assumes a general vdW distance of 0.105 nm when solvating. This default works well for all-atom models but falls short for CG water beads. If not adjusted, water beads may be placed too close to each other or to solute atoms, causing instability in energy minimization or strange solvent densities that could skew results.
What’s the solution?
The GROMACS Wizard in SAMSON allows you to solve this pain point directly from the interface by redefining the vdW distance used during the solvation step. Here’s how to use this feature effectively when prepping a CG system generated using the MARTINI v3.0.0 force field:
- In the Prepare tab, ensure your CG system is recognized (e.g., via Martinize2).
- Check Add solvent, and click the gear icon
to open the solvation settings. - In the pop-up window, increase the van der Waals distance to around
0.21 nm. This helps prevent overlapping beads and ensures a more realistic solvent distribution.
Adjusting this setting is straightforward but powerful: it helps ensure the initial structure is energy-minimizable and forms the basis for stable dynamics later. This small tweak can save you hours by preventing re-runs due to initial crashy conditions.
Why does it matter?
Coarse-grained models trade resolution for efficiency. While this helps speed up simulations dramatically, it’s easy to forget that some default parameters—especially those rooted in all-atom assumptions—no longer make sense. Solvent placement is one of them.
And if you’re planning to neutralize your system or add additional ions later, remember: GROMACS replaces solvent molecules with ions. So if your solvent is badly placed to start with, ion insertion can be problematic too.
Quick Recap
- Traditional vdW defaults are not optimized for CG systems.
- SAMSON’s GROMACS Wizard lets you easily adjust this when solvating.
- Use a vdW distance of at least
0.21 nmfor MARTINI water beads to avoid clashes. - Proper solvation leads to more stable minimizations and equilibrations downstream đź’§
To dive deeper into preparing coarse-grained systems using GROMACS Wizard in SAMSON, consult the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.