VMD-L Mailing List

From: Alexandre PERRET (alexandre.perret_at_etudiant.univ-reims.fr)
Date: Thu Dec 05 2013 - 04:31:55 CST

Hello VMD users,

I found something a bit odd using the hbonds plugin. According to the plugin, the criteria for the formation of a hydrogen bond are the distance between the donor D and the acceptor A and the angle D-H-A. The cut-off angle is by default 20 degrees, which means that D and A are too close to each other. In my opinion, it should be the angle H-D-A with a cut-off angle of 20 degrees. What do you think ?

Thank you in advance,
Alex 

--
Alexandre Perret
PhD Student
Groupe de Spectrométrie Moléculaire et Atmosphérique - UMR CNRS 7331
Université Reims Champagne-Ardenne
Campus Moulin de la Housse - BP 1039
51687 REIMS FRANCE
alexandre.perret_at_etudiant.univ-reims.fr
Tél : (+33/0) 3 26 91 33 66
Fax: (+33/0) 3 26 91 31 47