VMD-L Mailing List

From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Thu Dec 08 2016 - 17:01:17 CST

This is an issue that comes up every few years, see for example http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/19664.html <http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/19664.html> or http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/15715.html <http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/15715.html> . The short answer is that hbonds that cross periodic boundaries do not get counted.

Best,
JC

> On Dec 7, 2016, at 1:16 AM, Ern Ong <Ern.Ong_at_student.adfa.edu.au> wrote:
>
> JC,
> Thanks for your reply. May I know whether periodic boundary condition is a concern? Can it cause artefact in the hbond calculation?
>
> Thank you.
>
> Regards,
> Ernest
>
> From: JC Gumbart [mailto:gumbart_at_physics.gatech.edu <mailto:gumbart_at_physics.gatech.edu>]
> Sent: Wednesday, 7 December 2016 4:54 PM
> To: Ern Ong; Karteek Kumar
> Cc: Vmd l
> Subject: Re: vmd-l: VMD HBonds plugin
>
> VMD should guess the bonds when you load the file based on a distance criterion. You should visually inspect it. Assuming the guess is correct, it should be sufficient for determining hbonds.
>
> Best,
> JC
>
>
> On Wed, Dec 7, 2016, 12:10 AM Ern Ong <Ern.Ong_at_student.adfa.edu.au <mailto:Ern.Ong_at_student.adfa.edu.au>> wrote:
> Without the bond and angle information, then how VMD Hbonds plugin determines which one is hydrogen donor / acceptor?
>
> From: Karteek Kumar [mailto:karthik3327_at_gmail.com <mailto:karthik3327_at_gmail.com>]
> Sent: Wednesday, 7 December 2016 3:24 PM
> To: Ern Ong
> Cc: Vmd l
> Subject: RE: vmd-l: VMD HBonds plugin
>
> You can use it
>
> On 6 Dec 2016 23:18, "Ern Ong" <Ern.Ong_at_student.adfa.edu.au <mailto:Ern.Ong_at_student.adfa.edu.au>> wrote:
> Hi Karteek,
>
> 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…
>
> Regards,
> Ernest
>
> From: Karteek Kumar [mailto:karthik3327_at_gmail.com <mailto:karthik3327_at_gmail.com>]
> Sent: Wednesday, 7 December 2016 3:08 PM
> To: Ern Ong
> Cc: vmd-l_at_ks.uiuc.edu <mailto:vmd-l_at_ks.uiuc.edu>
> Subject: Re: vmd-l: VMD HBonds plugin
>
> 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 <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 <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.
>
> Thank you.
>
> Regards,
> Ernest