From: Josh Vermaas (
Date: Mon Sep 29 2014 - 09:14:02 CDT

Hi Phan,

You can use the PBCtools plugin
( to rewrap your
trajectory. If you just care about the hydrogen bonds between proteins,
what you should be able to do is use something like this:

pbc wrap -all -sel "protein" -center com -centersel "some atomselection
text that only picks out one of the two protein copies"

Then the selected protein will be near the center, and any of the atoms
involved in hydrogen bonding should be inside the same unit cell. Read
the documentation, and play around to see which combination of options
you prefer.

-Josh Vermaas

On 09/29/2014 08:09 AM, Vy Phan wrote:
> Dear Vmd users,
> My systems for MD simulations included 2 protein, but after 50ns of
> trajectory, one protein go out side the water box (sometimes
> comeback). I knew why this phenomenon happened but when I do not know
> how to analyze the result.
> I have problem when I calculated hydrogen bonds between two protein.
> Because of the boundary condition, the result of hydrogen bonds is not
> right. How can I solve this problem?
> Thank a lot and best regards,
> Phan Vy