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VMD: recalculate bonds during animation

In case you observe strange (long distance) bonds while animating a trajectory with VMD, this might be due to rearrangements of the molecule structure during the animation’s time frame. Sometimes, this behavior is not useful – especially, if you have lots of those conformation variations. In order to disable the bond caching during the animation, you can add the following lines to your .vmdrc:

# update bonds during animation
proc adj_bonds {args} { 
    mol bondsrecalc [lindex $args 1]
    display resetview 
trace add variable ::vmd_frame write adj_bonds