When preparing biological systems for molecular dynamics simulations, one recurring dilemma is deciding which water molecules to keep—and which to remove. Some crystal waters are tightly bound or functionally important, especially in active sites. Others are just noise, cluttering your system and slowing your calculations.
Fortunately, SAMSON’s GROMACS Wizard offers a way to selectively remove only the unnecessary waters, while preserving those that matter for biochemical interactions. This method can help ensure that you’re not over-simplifying your model while still keeping it efficient.
Why does this matter?
Removing all water molecules might simplify the system, but it risks deleting essential structural or catalytic components. Binding site waters, for example, can mediate interactions or participate in stabilization. On the other hand, keeping all crystal waters leads to bloated files and longer simulation times. The challenge is finding the balance.
The GROMACS Wizard in SAMSON makes it convenient to carry out a more targeted cleanup.
Step-by-step: How to delete only waters outside of the active site
- Select the relevant part of the active site—this could include ligands, residues, cofactors, or atoms that form the region of interest.
- Right-click on your selection in the Document view or Viewport, then go to Expand selection > Advanced.
- In the dialog that opens:
- Set Water as the Node Type.
- Choose the option beyond a certain distance (e.g., 5 Å), relative to your active site selection.
- Optionally, activate the Auto-update checkbox to visualize the selected waters in real-time before confirmation.
- Click OK to finalize your selection.
- Finally, right-click on the selection (again, either in the Document view or the Viewport) and choose Erase selection.
This workflow allows you to surgically remove waters that are too far from the active site to be relevant while keeping those that might play functional roles. It adds just the right amount of control without manual atom-by-atom deletion.
What does it look like?
Here’s what the expanded selection dialog setup looks like when you want to keep waters within 5 Å of a ligand, and select all others for erasure:
This seemingly small step can make a large difference in both the quality of your simulations and the time they take to run.
Learn more in the full documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at www.samson-connect.net.