When preparing molecular systems for simulations, small details can make or break the accuracy of your results. One such detail involves water molecules, particularly when they are outside the active site of interest. If you have crystal waters that don’t contribute to your simulation’s functionality, removing them can simplify your setup and eliminate unnecessary computational burden. Here’s a practical guide on how to use SAMSON’s GROMACS Wizard to accomplish this efficiently.
Why Remove Water Outside the Active Site?
Crystal waters are often present in Protein Data Bank (PDB) files. While some water molecules serve critical roles, such as stabilizing the protein’s structure or participating in enzyme catalysis, others are simply remnants that can interfere with your simulation. Carefully removing only the irrelevant waters ensures computational efficiency without compromising system accuracy.
Step-by-Step Guide to Selectively Remove Water Beyond an Active Site
- Select the Active Site
Start by selecting structures, residues, or atoms in the active site. You can do this through the Document view or the Viewport by manually highlighting relevant components. - Expand Your Selection
Right-click on the active site selection in either the Document view or the Viewport. In the context menu, navigate to Expand selection > Advanced. - Specify the Parameters
In the dialog box that appears, set Water as the node type you wish to target, and define a distance “beyond” the active site—essentially, how far out you want to include water molecules. Use the auto-update option to visualize your selection dynamically. Once satisfied, click OK to confirm. - Verify and Erase the Selected Water
Carefully review the selection to ensure accuracy. Once verified, right-click on the selected waters in the Document view or Viewport and choose Erase selection to remove them.
Things to Keep in Mind
Some water molecules might play critical roles, such as tightly bound waters or active-site waters that are functional in catalysis. Be cautious when identifying which waters to remove. If you’re uncertain, consider consulting prior literature on your system or experimenting with and without these waters to see their impact on simulation results.
Conclusion
Selective removal of irrelevant water molecules is an important preprocessing step that ensures your simulation maintains accuracy while minimizing computational load. By following the steps outlined above, you can efficiently clean your molecular system in SAMSON using the GROMACS Wizard. For more details, check out this section of the original documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.