From: Mert Gür (
Date: Sun Jan 24 2010 - 13:17:09 CST

Dear all,
I have performed MD in water and loaded my trajectory file into VMD. I can
see the hydrogen bonds by selecting "within 3 of protein" and "hbonds" as
the drawing method (Unfortunately I also see the hydrogen bonds among water
molecules.Also a solution for that would be nice)
I would like to determine for each time frame how many hyrdogen bonds there
are between the protein and the water molecules of the solvent.
Thanks in advance,

Mert Gur
Koc University