When setting up coarse-grained (CG) simulations in GROMACS, preparing the system correctly is essential—and solvent addition is a step that is often glossed over, or improperly configured. If you’re working with MARTINI-based CG models, especially those generated by Martinize2, there’s one subtle but crucial point that can make or break your system stability: setting the van der Waals (vdW) distance during solvation.
By default, GROMACS uses a vdW distance of 0.105 nm when adding solvent molecules. That value works fine for atomistic simulations but is far too conservative for CG models, where each water bead typically represents four water molecules. This mismatch may lead to overlapping beads and unnatural densities that can destabilize your simulation.
How to Fix It in SAMSON’s GROMACS Wizard
If you are using the GROMACS Wizard Extension in SAMSON, you have an opportunity to configure this correctly through a user-friendly interface.
- Once you have loaded your CG system (structure and topology files), check the Add solvent option in the Prepare tab.
- Click on the gear icon next to it to open the solvent options window.
- Increase the default vdW distance to 0.21 nm (or higher depending on the size of CG beads). This provides enough buffer space to prevent overlaps.
- Don’t change the other options unless you have a specific custom solvent model.
This simple change ensures that solvent packing is appropriate for CG simulations, helping you avoid bottle-necks during energy minimization or heating steps.
Remember that ions, if needed, are added by replacing solvent molecules. So activating solvent addition is a prerequisite for neutralizing your system or achieving a target salt concentration.
Why It Matters
Users often experience early crashes or instability during minimization because water beads end up too close to solute beads. These issues can be time-consuming to troubleshoot and are avoidable with a minor adjustment to vdW distance during solvation.
Finally, by configuring your solvent correctly, especially with the CG nature in mind, you enable a smoother simulation process—leading to faster, more reliable coarse-grained simulation workflows.
Learn more in the full documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.