Removing every water molecule can make a structure look tidier, but it may also remove waters that are part of the system you want to study. The challenge is to clear out unwanted crystal waters without accidentally deleting tightly bound or active-site waters. A selective cleanup lets you make that distinction before continuing with GROMACS preparation.
This walkthrough uses SAMSON’s GROMACS Wizard and the 1AKI structure as an example. The same selection approach can be useful whenever you want to remove waters far from a region of interest while preserving nearby ones.
Start with the region you want to preserve
Load your structure in SAMSON, then identify the active site or other region whose nearby waters you want to keep. Select one or more suitable structures, residues, or atoms in that region. For example, you might select a ligand, if one is present, or atoms that define the site. The selection is important: the next step uses it as the reference for finding waters by distance.
Select waters beyond the site
- Right-click the current selection in the Document view or the Viewport.
- Choose Expand selection > Advanced.
- In the dialog, set the node type to Water and choose beyond a distance from the selected region.
- Use auto-update if you want to preview the selection as you adjust it. Then click OK.
- Inspect the selected waters before deleting anything. If the selection is appropriate, right-click it and choose Erase selection.
The distance is a choice you make for your system, not a universal rule. The example image shows a selection beyond 5 Å, but that value should not be treated as automatically correct for every structure or research question. Preview the selection and check whether waters you intend to retain are included before erasing anything.
Why previewing matters
Crystal structures can contain waters with different roles. Some may be distant from the site you care about; others may be tightly bound or functionally important. A distance-based selection helps separate waters by location, but it does not determine biological importance for you. Treat it as a way to create a candidate selection, then verify the result in the molecular view.
It is also worth keeping the workflow consistent. If you have deliberately preserved selected waters, avoid subsequently applying a blanket Remove water cleanup that would remove them too. The general Home > Prepare cleanup includes options such as removing alternate locations, unnecessary small molecules, water, and monatomic ions. Choose options according to the contents you actually want in your simulation. In particular, do not remove ligands or cofactors that you intend to simulate.
A practical check before moving on
After cleanup, confirm that the active site still contains the waters you meant to preserve and that the distant waters you chose to remove are gone. Also check that the other molecules required for your intended system remain. This quick review can prevent an avoidable mismatch between the structure you prepared and the system you meant to simulate.
Once the structure is ready, continue to the GROMACS Wizard’s Preparation step to define the simulation model, box, solvent, ions, and project files. For the full preprocessing walkthrough, including the general cleanup options, see the original documentation page.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.