VMD-L Mailing List

From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Tue Dec 06 2016 - 23:54:08 CST

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> 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]
> *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> 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]
> *Sent:* Wednesday, 7 December 2016 3:08 PM
> *To:* Ern Ong
> *Cc:* 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
>
>
>
> 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
>
>
>
>
>