From: Vy Phan (
Date: Mon Sep 29 2014 - 08:09:02 CDT

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
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