From: Josh Vermaas (
Date: Mon Sep 15 2014 - 12:10:47 CDT

Molecule in the VMD sense, not molecule in the chemistry sense. If you
load two different systems at the same time, VMD treats these
independently, and that is the "molecule" boundary you can't cross (it
would also make no sense to try and find a hydrogen bond between two
independent structures).


On 09/15/2014 01:45 AM, maryam atabay wrote:
> Hi Dear all
> at page 113 of vmd tutorial Version 1.9.2beta1 with hbonds subjects,I
> can not understand the meaning of this sentence exactly:(The two
> selections must be from the same molecule.),with respect to we can
> have 2 different selection for donor and acceptor in 2 different
> molecule, how can you explain it?
> regards: Maryam
> --
> Maryam Atabay
> Ph.D in Nano Computational Chemistry,
> Molecular Simulation Lab, Azarbaijan Shahid Madani University,
> Tabriz,Iran.
> Email: <>