When preparing a molecular system for simulation, especially with tools like GROMACS, one of the early and often overlooked steps is deciding which crystal waters to keep and which to remove. This may seem straightforward at first—just remove all water molecules to make things easier, right? Not quite.
Crystal waters often include tightly bound or functionally important molecules, particularly in enzyme active sites or binding pockets. Removing all of them indiscriminately can impact the accuracy of your simulation. So how can we retain only the relevant waters and cleanly remove the rest?
Selective Water Deletion in SAMSON
With the GROMACS Wizard in SAMSON, there’s a practical approach to removing non-essential water molecules while preserving those that are critical to your study.
Step-by-Step Process
- Select Your Region of Interest: In the active site or another area where functional waters might be found, select the atoms, residues, or molecules (such as ligands or substrate) that define this region.
- Expand the Selection: Right-click on your selection in the Document View or Viewport, then choose Expand selection > Advanced. This brings up a dialog with options to specify nearby water molecules.
- Define Distance Criteria: In the dialog, set the node type to Water and use the spatial filter “beyond some distance”—e.g., beyond 5 Å—to select waters outside your region of interest. You can enable auto-update to preview your selection before applying it.
- Erase Unnecessary Waters: After verifying the selection, right-click and choose Erase selection. This removes distant water molecules but keeps those within your defined boundary.
This method is particularly useful if you are working on systems with known active sites or protein-ligand complexes, where maintaining key water-mediated interactions is important.
Why It Matters
Preserving structurally or functionally relevant water molecules ensures more realistic simulations, especially when modeling hydrogen bonding networks or particle dynamics within a confined site. Functional waters are often involved in catalysis, stability, or ligand binding—and they’re not always easy to add back once removed.
This careful pruning of water content is a small but important part of preparing your system for GROMACS simulations, and it can improve both accuracy and interpretability of your results.
Visual Example
As shown above, SAMSON’s visual interface allows you to not only select specific atom types, but also preview their spatial relationships before final deletion—minimizing the risk of unintended losses.
Additional Resources
To explore this process in more detail and see how it fits into the broader pre-processing workflow, visit the full documentation page: GROMACS Wizard – Pre-processing of the system.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.