VMD-L Mailing List
From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Sun Aug 24 2014 - 01:28:22 CDT
Easiest way to find your answer is to have a look at the source for the saltbr plugin (this is well worth doing, because learning a bit of TCL is invaluable when you want to start doing your own analyses). You’ll find it at /path/to/vmd/plugins/noarch/tcl/saltbr1.1/saltbr.tcl and the bit you’re looking for starts at line 790.
From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of Dawid das
Sent: Sunday, 24 August 2014 4:56 AM
Subject: vmd-l: How does saltbr calculate distance?
Dear VMD experts,
I have technical question about calculating salt bridges in VMD. When VMD plots the distance between let's say GLU7 and ARG56 as a function of time, what distance it actually is? Between what atoms of these residues? Or is it distance between centers of mass of negative and positive charge?