VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Apr 22 2010 - 10:30:17 CDT

Hi,
  We now have "pbwithin" selections and other PB related updates, but
"measure contacts" and "measure hbonds" code are not PB-aware yet.

Cheers,
  John

On Tue, Apr 20, 2010 at 11:07:29PM +0800, yongpingzeng wrote:
> Dear VMD users:
> I encounter with the issue of handling periodic boundary conditions
> while detecting Hydrogen bonds for pure water. For instance, the command
> 'measure hbonds' is not aware of PBC, and will miss whatever bonds may
> extend across the edges of the periodic box.
> Jonh Stone have given some hints:
> In the post in 2005
> > existing VMD functions that do:
> > - 'within' and 'exwithin' atom selections
> > - 'measure contacts'
> > - 'measure hbonds'
> > - automatic bond search (allow bonds across PBC cell boundaries)
> > - draw bond components of the Bonds, CPK, and Licorice representations
> > - draw dynamic bonds representation
> >
> > Adding PBC-awareness to the drawing code is the most risky in terms
> > of hurting performance, but this may be something that could be dealt
> with
> > by adding a checkbox so that VMD only spends effort checking for this
> when
> > the user actually needs it.
> >
> > Before embarking on implementing all of this, it wvmd-l_at_ks.uiuc.eduould
> be nice to know
> > which of these users would find most beneficial. We could work on the
> > most-wanted features first...
> >
> > John Stone
> I dont know if the problem have been resolved? Could anyone like to give
> me some help?
>
> Best
> Yongping Zeng
> Yangzhou University 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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