When preparing a biomolecular system for simulation in GROMACS, one often encounters the need to remove water molecules — typically those originating from crystal structures in the Protein Data Bank (PDB). In many cases, however, not all water molecules should be removed. Some waters are functionally important, residing in active sites or coordinating metal ions, and their removal could compromise the biological relevance of your simulation. But doing this manually can be tedious and error-prone.
Thankfully, the GROMACS Wizard in SAMSON helps streamline this process through a simple and visual interface, allowing you to precisely eliminate only the waters you don’t need—while preserving those that matter.
Why this matters
Crystallographic waters in PDB files might include several that are randomly placed or loosely bound. These waters add noise and may interfere with solvation or topology generation for GROMACS. On the other hand, many systems (such as binding pockets) feature tightly bound or conserved water molecules that are integral to function or structure. Selectively keeping only these makes your simulations cleaner and more realistic.
A guided way to remove only unnecessary waters
Here’s how you can delete only water molecules that are outside of your active site using SAMSON’s GROMACS Wizard:
- Start by loading your structure, e.g., the 1AKI protein structure, via Home > Fetch and entering “1AKI” in the PDB dialog.
- Once loaded, select the important structures in your molecule—ligands, water molecules, atoms—in or around the active site. You can do this from the 3D Viewport or the Document view.
- Right-click your current selection, then go to Expand selection > Advanced.
- In the dialog that opens, choose Water as the Node type and set a distance like
beyond 5Åto select water molecules far from your region of interest. You can enable auto-update to preview your selection. - After confirming, right-click on the new selection and choose Erase selection to remove only those water molecules outside your active site.
This approach gives you full control over which waters to keep or discard — a big improvement over removing all water molecules with a single checkbox.
Pro tip: Use selections creatively
Selections in SAMSON are highly flexible. You’re not limited to water: select cofactors, ligands, or any structures relevant to your simulation. The key is using the Expand selection tool effectively. Distances can be customized based on your system’s dimensions and interaction network.
Conclusion
Selectively removing water molecules might sound minor, but it can have a real impact on the accuracy of your simulations. Doing it manually in a PDB file can be tedious, occasionally imprecise, and even irreversible. With SAMSON’s GROMACS Wizard, you can visually select and erase unwanted molecules in seconds—keeping your system clean and biologically meaningful at the same time.
To learn more about pre-processing workflows in GROMACS Wizard, check out the full documentation here:
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.