From: Ana Celia Vila Verde (
Date: Mon Sep 29 2014 - 09:21:18 CDT

Dear Phan Vy,

You will need to re-calculate the coordinates of each atom at each frame
so that the protein is at the center of the box in each frame. You can
do this using the pbctools in VMD
( Because this
may be somewhat time-consuming, you may want to save the new trajectory
in a new dcd file using the command animate.



On 29/09/14 15:09, 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