VMD-L Mailing List
From: Ern Ong (Ern.Ong_at_student.adfa.edu.au)
Date: Tue Dec 06 2016 - 22:17:45 CST
Thanks for the reply but I think my question is not answered.
My question is whether this .xyz output file can be used to determine the number of hydrogen bonds in the simulation box? Since .xyz file does not include the bond and angle information…
From: Karteek Kumar [mailto:karthik3327_at_gmail.com]
Sent: Wednesday, 7 December 2016 3:08 PM
To: Ern Ong
Subject: Re: vmd-l: VMD HBonds plugin
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,
On Tue, Dec 6, 2016 at 10:38 PM, Ern Ong <Ern.Ong_at_student.adfa.edu.au<mailto: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.