VMD-L Mailing List

From: Olaf Lenz (olenz_at_fias.uni-frankfurt.de)
Date: Thu Apr 17 2008 - 04:32:34 CDT

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Ana Vila Verde wrote:
> 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.

What I would probably do in this situation is to split the box into
eight domains (2 subdomains in each dimension), and the to loop over all
of these subdomains:

1. Wrap all atoms into a box that is centered on the subdomain, by using
"pbc wrap -center $x $y $z", where (x,y,z) is the center of the subdomain.
2. Now measure all hbonds between all oxygens in this box and all
hydrogens of the system. The selection for the oxygens will look
something like
"name O and x > 0 and x < 5 and y > 0 and y < 5 and z > 0 and z < 5"
for the first subdomain of a 10x10x10 box.

If you do this for all 8 domains, you should have all hbonds in the system.

Olaf
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