VMD-L Mailing List

From: David Carrasco de Busturia (davidcarrascobustur_at_gmail.com)
Date: Thu Aug 18 2022 - 05:41:30 CDT

This question refers to the `Angle Cutoff` variable for hydrogen bonds
detection in vmd.

Consider the water dimer posted here:
https://urldefense.com/v3/__https://github.com/DavidCdeB/H-bonds__;!!DZ3fjg!_zzd0T13G69_pKop_G6jmXTL9LemaGAIpEaeoRyf-Q_jq74VTn7zdzB7NA8umDEY9371WXK9tnqgOyH_KD0ZLJ4s5Zmu$

I've marked the `a`, `b` and `c` angles for the hydrogen bond.
(where the numeric values shown are those that appear in the terminal
window when measuring them with vmd).

The hydrogen bond is not detected for `Angle Cutoff = 29` but it is
detected for `Angle Cutoff = 30` (see figures in the post)

I'm wondering which is this `Angle Cutoff` that VMD is referring to since
30 does not seem to match any of the angles marked in the image.