I am working on the visualization of an MD trajectory where some water molecules are broken due to PBC artifacts, causing oxygen and hydrogen atoms to be separated over large distances. To address this, I currently use the following workflow:
Remove all bonds in water molecules near the ligand.
Rebuild only reasonable bonds, avoiding artifactually long bonds.
Remove water atoms that have no bonds per frame:
This works well to fix visualization artifacts, but the workflow is computationally heavy, as it rebuilds bonds in every frame. Is there a way to achieve the same in a single step by simply removing waters with stretched bonds?
Many thanks in advance!
Enrico