One common challenge in preparing biomolecular systems for simulation is managing water molecules. While bulk solvent can be added systematically during solvation, crystal waters—those resolved in the original structure—often have functional roles, especially around the active site of biomolecules. Automatically removing all water molecules might strip away those that contribute to catalysis or structural stability.
In this post, we’ll walk through how to remove only the non-essential crystal waters in SAMSON’s GROMACS Wizard, allowing you to preserve the ones relevant for your simulation—without manual atom-by-atom editing. This is particularly useful for users who are preparing systems with tightly bound water within the active site and want more control over system preprocessing.
Why this step matters
Removing all waters can introduce errors in simulations by stripping out structurally or functionally important molecules. On the other hand, not removing unnecessary waters increases system size and simulation time. The ideal scenario? Remove only what’s unnecessary.
How to selectively remove water outside the active site
- Select the active site environment.
In the Document view or the Viewport, select residues, atoms, or molecules that form the active site. This can include a ligand, catalytic residues, or tightly bound waters. - Expand the selection with Smart Filters.
Right-click on the current selection → Expand selection > Advanced. - Configure advanced selection settings.
In the pop-up dialog:- Set Node type to
Water - Choose beyond a distance (e.g., 5 Å) from the current selection
- You can enable
auto-updateto preview the selection dynamically
Click OK.
- Set Node type to
- Confirm and delete.
Review the selected waters visually to confirm they are indeed outside your region of interest. Then, right-click and choose Erase selection.
When should you keep crystal waters?
If the structure you’re working with includes water molecules that are hydrogen bonded to ligands, bridge metal ions, or have low B-factors (high confidence in interpretation), it is worth preserving them. They might actively participate in interactions or stabilize the structure.
This method gives you a balanced approach—removing unnecessary waters while retaining critical components of your system, helping to improve both accuracy and efficiency in your GROMACS simulations.
To see the full documentation for preprocessing with SAMSON’s GROMACS Wizard, visit the official tutorial page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.