From: John Stone (
Date: Thu Dec 08 2005 - 13:40:13 CST

  We should probably create new PBC-aware versions of the
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 would be nice to know
which of these users would find most beneficial. We could work on the
most-wanted features first...

  John Stone

On Thu, Dec 08, 2005 at 04:03:57PM +0100, Jérôme Hénin wrote:
> Dear VMDers,
> I suppose some of you have stumbled upon the issue of handling periodic
> boundary conditions while detecting hydrogen bonds. 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.
> The only thing I have come up with so far is the following:
> 1) use 'measure hbonds'
> 2) translate a part of the system by a periodic repeat distance, so that two
> of the edges are not edges anymore
> 3) 'measure hbonds', again
> 4) repeat 2) and 3) until all the edges have been properly treated
> 5) remove all the multiple-counting that we have done
> That is kind of a heavy procedure. Does anyone have a better idea?
> Thanks in advance,
> Jerome
> --
> Jérôme Hénin
> Equipe de Dynamique des Assemblages Membranaires
> Université Henri Poincaré / CNRS
> Tel : (33) 3 83 68 43 91 Fax : (33) 3 83 68 43 87

NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email:                 Phone: 217-244-3349
  WWW:      Fax: 217-244-6078