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)