VMD-L Mailing List

From: Jérôme Hénin (jerome.henin_at_uhp-nancy.fr)
Date: Thu Dec 08 2005 - 09:03:57 CST

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/