VMD-L Mailing List

From: Eduard Schreiner (eduard.schreiner_at_rub.de)
Date: Fri Dec 09 2005 - 04:41:10 CST

On Thursday 08 December 2005 20:40, John Stone wrote:
> Jerome,
> 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
> vmd_at_ks.uiuc.edu
>
> 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
> > http://www.edam.uhp-nancy.fr/
Hello John,
I agree with Lubos.
But since I am working in both areas, biomolecular and crystal related,
to me all of the above mentioned items would be very useful. These
functionalities would improve the already very powerfull 'vmd'.
Thanks a lot for all your time and work.

Eddi 

-- 
--
=======================================================================
Eduard Schreiner                        e-mail: eduard.schreiner_at_rub.de
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-22121
Ruhr-Universitaet Bochum - NC 03/52         Fax:   ++49 (0)234/32-14045
D-44780 Bochum                               http://www.theochem.rub.de
=======================================================================