VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Sun Sep 15 2013 - 17:11:27 CDT

Based on my own observations, colors are based on the name of the atom
that "owns" the hydrogen in the topology. By default, oxygens are red,
nitrogens are blue, and carbons are cyan (the lightish green). So a
"hydrogen bond" from a water hydrogen to ammonia would be red, but a
ammonia hydrogen that is shared with water would be a blue dashed line.
-Josh

On 09/13/2013 12:38 PM, Research Jubilant wrote:
> Hello all VMD users,
>
> I'm using VMD's hydrogen bond capability from the Graphical
> Representations tool. I get the Hbonds displayed in different colors
> (mainly blue, red and light green, which is the VMD's default color
> when any molecule is loaded) when I colored them by default 'Name'. I
> checked the previous discussions about it in the forum and also in
> userguide but no helpful information.
>
> Does anyone clarify the meaning of the colors shown in VMD for Hbonds?
>
> Thanks
>
> J