One of the crucial but often overlooked steps in molecular simulations with GROMACS is deciding which water molecules to include and which to remove from your system. While it might be tempting to wipe them all and let GROMACS solvate the system from scratch, some water molecules—especially those in the active site—perform specific structural and functional roles and should not be discarded lightly.
Water molecules in crystal structures can be tightly bound, mediate key interactions, or be functionally relevant. Discarding them without scrutiny can lead to incorrect simulation results. On the other hand, leaving too many irrelevant waters, especially those crystallized far from regions of interest, can unnecessarily complicate your system and increase computational load.
Selective Water Molecule Removal in SAMSON
The SAMSON GROMACS Wizard provides a straightforward method to selectively remove water molecules outside of a region of interest, such as the active site. This ensures that your simulation focuses on functionally relevant interactions, while still reducing noise and system size.
How to Remove Unnecessary Waters, Step by Step
- Select the structures in the active site (e.g., ligands, residues, or atoms that define your region of interest).
- Right-click on this selection in the Document view or Viewport, and choose Expand selection > Advanced.
- In the pop-up dialog, set the node type to Water, and choose a distance criterion (e.g., “beyond 5 Å”). You can enable auto-update to preview your resulting selection.
- Once satisfied, click OK. Then right-click on the selected waters in the Document view or Viewport and select Erase selection.
This approach allows precise control over the representation of your biological system, preserving key water molecules while minimizing the rest.
Why It Matters
Removing all water molecules indiscriminately might save time, but it risks eliminating waters that play a structural or catalytic role. Conversely, keeping all water molecules might bloat your system size and impact simulation performance. This selective deletion workflow promotes better simulation accuracy without overburdening resources.
More nuanced, science-based decision-making is critical in molecular modeling. SAMSON’s built-in tools allow you to make these decisions visually and interactively, making it easier to balance biological relevance with computational efficiency.
To learn more about pre-processing your system with the GROMACS Wizard, including ligand removal, topology generation, and hydrogen management, visit the full documentation: https://documentation.samson-connect.net/tutorials/gromacs-wizard/preprocess/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.