From: Ana Vila Verde (
Date: Thu Apr 17 2008 - 02:54:08 CDT

Dear VMD users,

I am trying to use the command measure hbonds to calculate the number of
hbonds between a molecule and water from a simulation with PBCs.
However, very often my molecule "sticks out" of the water box, and when
that happens I get an inaccurate count of hbonds. I checked the mail
list archive for a possible solution and didn't find any. I also don't
think that unwrapping my trajectory is a solution to the problem,
because the density of the "real" water molecules will be lower around
my molecule and I will also not get an accurate count.

I thought I'd ask whether any of you would share a script to get around
this problem before I go and code my own.

Thank you for you attention. Best regards,


Ana Vila Verde
Post-doctoral scholar
FOM Institute for Atomic and Molecular Physics [AMOLF]
P.O.Box 41883
1009 DB Amsterdam
The Netherlands
Phone: +31-20-6081392
Fax: +31-20-6684106
University of Minho
Physics Center
Campus de Gualtar
4710-057 BRAGA