delete_drude_waterbonds 1.0 ---------------------------- REQUIREMENTS: VMD Version 1.9.4 or greater DESCRIPTION: Removes spurious H1-H2 bonds in SWM4 (Drude polarizable) water residues loaded in VMD. When PSF files for Drude force field systems are read into VMD, artificial bonds between the two hydrogen atoms (H1 and H2) of SWM4 water molecules may appear in the bond list. This script efficiently identifies and deletes those H1-H2 bonds while preserving all other bonding topology. Uses O(1) hash-based lookup for fast filtering and performs a single bulk reassignment of the bond list for optimal performance on large systems. PROCEDURES: Source the script after loading a Drude force field system (PSF/DCD). It operates on the top molecule automatically and reports the number of deleted bonds. EXAMPLE USAGE: # Load your Drude polarizable system mol new system.psf mol addfile trajectory.dcd waitfor all # Remove spurious H1-H2 bonds in SWM4 waters source delete_drude_waterbonds.tcl DOWNLOAD THE FILE: delete_drude_waterbonds.tcl AUTHOR: Diego Enry Barreto Gomes (dgomes@auburn.edu)