How to Delete Only the Right Water Molecules Before a Simulation

Removing water molecules before running a molecular dynamics simulation can be more complicated than it sounds. For molecular modelers working with crystal structures, deleting all waters indiscriminately can result in the loss of functionally important waters, especially those located in active sites or involved in key interactions. On the other hand, keeping too many can unnecessarily increase system size and computational cost.

Luckily, the GROMACS Wizard in SAMSON offers a more refined approach. Instead of wiping out all existing crystal waters, you can selectively remove only the water molecules that are located outside a defined region—like the system’s active site. This post walks through the steps to do just that.

Step-by-step: Deleting Waters Outside the Active Site

  1. Select what matters: Start by selecting the functional part of your system, such as ligands or active-site residues. Simply click on these atoms or residues in the Viewport or the Document view.
  2. Expand the selection strategically: Once selected, right-click your selection and go to Expand selection > Advanced in the context menu.
  3. Define your cleanup rule: In the pop-up dialog, choose Water as the Node type. Then, specify a distance (e.g., beyond 5 Å) to target waters outside your selected region. Enable the auto-update checkbox to preview what’s being selected.
  4. Erase the excess: If the selection looks correct, click OK, then right-click the selection and choose Erase selection.

Expand selection: select water beyond 5A

Why is this important?

Including all crystallographic waters in a simulation can:

  • Skew electrostatic interactions, especially in ligand-binding regions
  • Lead to non-physical density distributions once solvating the system
  • Increase the number of atoms and simulation time significantly

However, removing key active-site water molecules can distort the biological relevance of the simulation. This approach finds a middle ground by preserving only the waters most likely to be important based on proximity to your region of interest.

Tips for Efficient Cleanup

  • Double-check your water selections visually before deletion.
  • Use multiple reference atoms (e.g., ligand + nearby residues) to define an active site region more comprehensively.
  • Be conservative about the distance threshold—sometimes 4–5 Å is more appropriate than larger cutoffs.

This technique is especially helpful for those working on enzyme simulations, binding free energy calculations, or modeling metal-coordinated systems, where local waters may play structural or catalytic roles.

To learn more about pre-processing systems in GROMACS Wizard, including additional filtering steps for ligands, ions, and alternate locations, visit the full documentation at this page.

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

Comments are closed.