Which Water Molecules Should You Keep for Molecular Simulations?

When setting up a biomolecular system for simulation, one recurring challenge for molecular modelers is deciding what to do with water molecules already present in crystal structures. Should you remove them all, keep them all, or try to distinguish the important ones from the incidental?

In SAMSON’s GROMACS Wizard, there’s an efficient way to selectively delete only those water molecules that lie outside of the active site—crucial for keeping functionally relevant water while cleaning up your system for simulation. Thankfully, this doesn’t require manual selection of hundreds of water molecules. Here’s a focused guide to solving this common preparation issue.

Why Does This Matter?

Crystal structures from the Protein Data Bank often come with many water molecules. While some play a role in active site chemistry—stabilizing interactions or participating in mechanisms—others exist just because they were trapped during crystal packing. Including or excluding the wrong ones can change your simulation results.

Manually analyzing each water molecule is not only tedious but also inefficient for larger systems. The GROMACS Wizard in SAMSON helps automate this part of the process.

How to Remove Non-Essential Water Molecules

To remove only those water molecules that are outside the active site, follow these steps in SAMSON:

  1. Select the atoms, residues, or molecules that define your active site. This could be the ligand and surrounding protein residues, for example.
  2. Right-click the selection in the Document view or Viewport and go to Expand selection > Advanced.
  3. In the dialog that opens, set the Node type to Water and pick a spatial filtering option such as “beyond 5-6 Å” from your active site. The auto-update feature helps preview your selection.
  4. Click OK to finalize the selection and verify it visually.
  5. Right-click the final selection and choose Erase selection to remove the unwanted water molecules.

Select and erase water molecules outside the active site

Tips for Better Results

  • Use biological knowledge: If you know certain water molecules are crucial (e.g., involved in hydrogen bonding with ligands), include those in your selection to preserve them.
  • You are not limited to geometry. You can combine this geo-selection with selection classes under Select > Biology > Water.
  • This process works best after an initial cleanup using Home > Prepare to remove alternate locations and non-essential molecules.

More Ways to Prepare Your System

Selective water deletion is just one of the options in the pre-processing workflow. The larger goal is to provide GROMACS with a system ready for reliable simulation. Consider also removing ions or ligands you don’t need, and review arbitrary molecules that need parametrization.

To learn more, visit the full documentation at https://documentation.samson-connect.net/tutorials/gromacs-wizard/preprocess/.

SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.

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