When preparing biomolecular systems for molecular dynamics using GROMACS, one frequent challenge is deciding which water molecules to retain. Automatically removing all crystallographic water may affect the behavior of key biological sites, especially if some of these water molecules are tightly bound or play a structural or catalytic role. But how do you keep functional waters while clearing unnecessary ones?
Fortunately, with the GROMACS Wizard in SAMSON, there’s a user-friendly way to identify and remove only those water molecules that are clearly outside a functional boundary — preserving the integrity of the active site while cleaning the rest of the system.
Why Not Just Delete All Waters?
Many simulation workflows recommend starting fresh with solvation. However, deleting all existing crystal waters can sometimes mean losing important parts of the biological system. Retaining relevant waters can significantly improve the realism and predictive power of your simulation. Think hydrogen-bonding networks and metal-coordinating waters.
Instead of manually searching and selecting each water molecule worth keeping, SAMSON’s interface makes it possible to perform a distance-based selection — ideal for keeping waters close to your ligand or active site.
Step-by-Step: How to Delete Only Non-Functional Water Molecules
- Ensure your active site (ligand, residues, or atoms of interest) is correctly selected in the Document view or Viewport.
- Right-click on the selection and choose Expand selection > Advanced.
- In the pop-up dialog that appears, set Water as the Node type. Then choose selection of water molecules that are beyond a specific distance (e.g., 5Å) from the active site.
- Click on auto-update to preview your selection live. When satisfied, click OK.
- Verify your selection and right-click on it in the Document view or the Viewport, then choose Erase selection.
This approach allows for precise cleaning of the system, giving you more control over the initialization of simulations.
Who Can Benefit?
This method is especially useful for:
- Researchers working with enzyme active sites where water is part of the catalytic mechanism
- Modelers preparing accurate protein-ligand complexes for free energy calculations
- Anyone trying to maintain biologically relevant starting structures before full solvation
Final Thoughts
Fine-tuning hydration in your system doesn’t need to be tedious. With SAMSON’s built-in tools, you can easily distinguish between functional and bulk crystal water. Reducing the chance of accidentally deleting important molecules improves the reliability and reproducibility of your simulations.
💡 Learn more in the GROMACS Wizard documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.