A protein structure can contain many water molecules, but “remove all waters” is not always a safe cleanup rule. Some waters may be tightly bound or functionally important, including waters near an active site. Removing them indiscriminately can change the structure you intended to prepare for simulation.
The practical challenge is to distinguish waters you do not need from those you want to preserve. In SAMSON’s GROMACS Wizard workflow, you can select waters by their distance from a chosen part of the system, erase only the selected waters, and then continue with preparation.
Start with the region you want to preserve
Load your system in SAMSON and identify the active-site region or another region whose nearby waters you want to keep. You can select structures, such as a ligand or water; residues; or individual atoms. The selection defines the reference region for the next step, so check that it contains the right part of the system before expanding it.
Select waters by distance
- Right-click the current selection in the Document view or the Viewport.
- Choose Expand selection > Advanced.
- Set Water as the node type, then choose waters beyond a distance from the selected region. The documentation image illustrates a 5 Å example; choose a distance appropriate to your system rather than treating that example as a universal cutoff.
- If useful, enable auto-update to preview the selection. Review it, then click OK.
- Inspect the selected waters before deleting them. Right-click the selection and choose Erase selection.
This approach gives you a chance to preserve waters close to the region you care about while removing waters farther away. The distance-based selection is a practical cleanup step, not a substitute for deciding which waters are important to your model. Verify the selection in the viewport or Document view before erasing it.
When broad water removal may be appropriate
For some systems, removing water during general cleanup may be suitable. The GROMACS Wizard’s Home > Prepare options include Remove water, alongside options to remove alternate locations, ligands, and monatomic ions. But if your system contains tightly bound or active-site waters that you want to retain, use a more selective approach instead of removing all water.
The same caution applies to other molecules: do not remove a ligand or cofactor that you intend to simulate. Cleanup is about removing components you do not need, not stripping the structure indiscriminately. Once the structure is cleaned, continue to the GROMACS Wizard preparation step to define the simulation model, box, solvent, ions, and project files.
A quick pre-deletion check
- Is the selection anchored to the active site or region you intend to preserve?
- Is the node type set to Water?
- Does the chosen distance select only waters you are willing to remove?
- Have you reviewed the selected molecules before erasing them?
These checks help avoid a common preparation mistake: treating every water molecule as disposable when some may matter to the system being modeled.
For the full workflow and additional cleanup guidance, see the GROMACS Wizard pre-processing tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.