From: John Stone (
Date: Wed Sep 02 2015 - 13:55:30 CDT

  While I'm no expert on this topic, my reading of online
refs indicates that 4.0A is really more of an upper bound.
That leads me to conclude that 3.2A was likely chosen as
a conservative distance that won't return false-positives,
given that (as I understand it) the code searches over many
frames in a trajectory and records a salt bridge if the distance
criterium is met for any pair in any frame. The best answer
would be obtained by contacting Elizabeth Villa or Leonardo Trabuco,
who co-developed this plugin. Elizabeth is now at UCSD:

  John Stone

On Fri, Aug 28, 2015 at 09:30:00PM +1200, LW wrote:
> Dear VMDers,
> I have a question on sal bridge.A
> In 'Ion-pairs in protein' by Barlow and Thornton, the salt bridges(ion
> pairs) were analysed with a 4.0 Angstrom distance criterium.
> On the webpage of VMD, the salt bridge cutoff distance was chosen to be
> 3.2 Angstroms by the plugin. Is there any reference to this? Why 3.2?
> Many thanks in advance.
> Levi

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