When preparing a biomolecular system for simulations in GROMACS, one common step is to remove water molecules from the structure. However, indiscriminately deleting all water can lead to the removal of functionally important or tightly bound waters, especially those located in or near the active site of a protein.
Why does this matter? Some water molecules mediate essential interactions, stabilize conformation, or participate in the mechanism of biological function. Removing them can introduce errors into your simulation, produce unrealistic dynamics, or entirely invalidate the biological relevance of your results.
Thankfully, SAMSON provides an easy way to only remove the waters you don’t need by selecting and deleting only those beyond the active site. Here’s how to do it step by step within the GROMACS Wizard for SAMSON:
Step 1: Select the Active Site
You’ll first need to select what’s considered functional in your system. This might include the ligand, known active-site residues, or already-identified structural waters.
- Click on Document view or select atoms directly in the Viewport.
- Select residues or atoms forming the active site (ligands, nearby residues, or any core water molecule).
Step 2: Expand the Selection to Find Surrounding Waters
SAMSON has a smart way to help you isolate distant water molecules. Just right-click the selection and navigate to:
Expand selection > Advanced
In the dialog box that pops up:
- Choose Water in the Node type.
- Select the beyond distance criterion, e.g., 5 Å.
- Enable the auto-update checkbox to visually inspect what’s being selected.
This lets you selectively find only the water molecules that fall beyond the active site vicinity.
Step 3: Delete Only Distant Water Molecules
After verifying your selection (this is crucial!), right-click again on the highlighted waters and select Erase selection. Your active-site waters stay untouched, and only the unnecessary water gets deleted. 🎯
Why This Matters
Preserving functional water is not just about keeping atoms—it’s about maintaining the biological and chemical fidelity of your system. This approach ensures your simulation setup remains realistic while keeping your system clean and simulation-ready.
To learn more about pre-processing systems in the GROMACS Wizard in SAMSON, see the full documentation here: GROMACS Wizard – Pre-processing of the system.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.