From: L. Michel Espinoza-Fonseca (
Date: Sun Mar 05 2006 - 18:06:50 CST

Dear all,

I've been trying to analyze the contacts between water and a given
peptide from my trajectories. I used a nice script provided by one of
the VMD users. Everything went well, except from the fact that VMD is
not able to count the water molecules around my peptide from the image
of my periodic box. I've read some issues related to the pbc and VMD
(computation of hbonds, for instance), and according to what I read,
there is not such handling of pbc in VMD. Do you have any suggestions?
I tried to use some artifacts such as drawing images of the water box,
but it didn't work.