Keeping the Essential: Selective Removal of Crystal Waters for GROMACS Simulations

When preparing a molecular system for simulation in GROMACS, one common yet delicate task is handling existing crystal water molecules. While some waters can safely be deleted, others—especially those tightly bound in functional sites—may be crucial to your system’s behavior. Removing all water molecules indiscriminately might compromise the biological relevance of your simulation.

The SAMSON GROMACS Wizard offers a method to remove only unnecessary water molecules while preserving those that are functionally important. Here’s how to do it, step-by-step, using SAMSON’s intuitive interface:

Why Selective Water Removal Matters

Crystal water molecules in PDB structures often include both structurally relevant waters—like those involved in stabilizing active sites—and others that are simply artifacts of crystallization conditions. In many cases, researchers want to remove the latter while keeping the former. Manual selection is time-consuming and error-prone, especially for large systems.

How to Keep Critical Waters and Remove the Rest

  1. Select functional areas. Start by selecting atoms, residues, or molecules that define the active site or the region you want to protect (e.g. the ligand and its surroundings).
  2. Use the Expand Selection tool. Right-click your selection in the Document view or Viewport. From the context menu, choose Expand selection > Advanced.
  3. Fine-tune your selection. In the dialog that appears:
    • Set the Node type to Water.
    • Choose the beyond option.
    • Set a distance threshold (e.g. waters beyond 5 Å from the active site).
    • Click auto-update to verify and preview the selection visually.
    • Click OK to confirm.
  4. Remove the selection. Right-click the selected water molecules and choose Erase selection. All distant, non-functional waters are removed.

Here’s what the interface looks like during the process:

Expand selection: select water beyond 5A

Pro Tips

  • If you’re unsure about the role of certain waters, consider visualizing hydrogen bond networks or referring to relevant literature before deleting them.
  • This selective deletion feature avoids unnecessary manual cleanup and ensures important structural components remain intact.

This approach improves your simulation setup with minimal effort and preserves the integrity of your model.

To learn more about this and other pre-processing steps in the GROMACS Wizard, see the full documentation page 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.

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