VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Aug 31 2011 - 13:27:21 CDT

On Wed, 2011-08-31 at 10:29 -0700, hamid mosaddeghi wrote:
>
>
> Dear Goldsmith
>
> Please explain "Hbonds in VMD use a very non standard angle"? what
> should I do to solve this problem? or how can I define these Cutoff
> angle 30 and cutoff distance 3.5 A exactly for software?

this has nothing to do with the cutoffs.

i already mentioned earlier, there are
different ways to define the h-bond angle,
and a lot of people arguing over which is
the right way to do it.

axel.

>
> Best Regards.
>
>
>
> From: ", Jacob" <jgoldsmith_at_uky.edu>
> To: hamid mosaddeghi <hamid592004m_at_yahoo.com>
> Sent: Wednesday, August 31, 2011 5:55 PM
> Subject: RE: vmd-l: Hbond in VMD
>
> Hbonds in VMD use a very non standard angle, not necessarily the angle
> your thinking of. Look at the source code for more information.
>
> -J
> ________________________________________
> From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
> hamid mosaddeghi [hamid592004m_at_yahoo.com]
> Sent: Wednesday, August 31, 2011 4:12 AM
> To: vmd
> Subject: vmd-l: Hbond in VMD
>
> Dear all
>
> I counted Hbond from VMD for SPC/E water model in normal condition , I
> got 2.56 Hbond per/molcule but more paper reported 3.~ 3.3 Hbond
> per/molcule why?
>
> I used Cutoff angle 30 and cutoff distance 3.5 A from literatures.
>
> Best regards
>
> Hamid Mosaddeghi
>
> Phd Student Of Physical Chemistry
>
>
>
>
>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.