From: Olaf Lenz (
Date: Mon Nov 14 2011 - 09:57:04 CST


On Mon 14 Nov 2011 03:48:42 PM CET, Hitesh Patel wrote:
> I have MD simulations trajectories of 3ns from desmond. but, after
> 2ns complex is going out of box. How can I wrap in a way, that
> everytime molecule stay at the centre of box. I tried "pbc wrap -all"
> but,it makes stretched bonds. After that I tried to unwrap. and again
> molecule looks out of box. What commands should I use ?

The pbctools cannot help you with that, because they move atoms only in
integer steps of the unit cell lengths, i.e. they do not physically
modify the system in any way. What you want is to recenter the whole
simulation box. You can do that by some Tcl scripting.


Dr. rer. nat. Olaf Lenz
Institut für Computerphysik, Pfaffenwaldring 27, D-70569 Stuttgart
Phone: +49-711-685-63607