VMD-L Mailing List

From: Karteek Kumar (karthik3327_at_gmail.com)
Date: Tue Dec 06 2016 - 22:07:46 CST

Hello Ernest,

Measuring the Hbond criteria in VMD is different than the conventional one.

In general Hbond angle: D-H-A ( for water, angle might be close to 180)

VMD measures, A-D-H ( here it is close to zero)

Go through http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/15069.html

It is just the convention, how VMD measures.

Hope it helps,

Thanks,
Karteek

On Tue, Dec 6, 2016 at 10:38 PM, Ern Ong <Ern.Ong_at_student.adfa.edu.au>
wrote:

> Dear VMD users,
>
>
>
> I have run a water simulation in LAMMPS and the output file format is
> .xyz, which does not include any bond and angle information. My question is
> whether this .xyz output file can be used to determine the number of
> hydrogen bonds in the simulation box? I have looked up VMD documentation
> and found this:
>
>
>
> A possible hydrogen bond is defined by the following criteria:
>
> Given an atom D with a hydrogen H bonded to it and an atom A with no
> hydrogen bonded to it, a hydrogen bond exists between A and H if the
> distance ||D-A|| < dist and the angle D-H-A < ang, where ang and dist are
> user defined.
>
>
>
> Thank you.
>
>
>
> Regards,
>
> Ernest
>
>
>