From: Axel Kohlmeyer (
Date: Mon Nov 14 2011 - 09:57:06 CST

On Mon, 2011-11-14 at 15:48 +0100, Hitesh Patel wrote:
> Hello,
> 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 ?

when using pbc wrap, make sure you have the right
'-compound' flag. the default is wrapping individual
atoms, which will result in those "stretched" bond.
to retain intact molecules, you should try to wrap
with '-compound fragment' added instead.


> Thanks,
> Regards,
> Hitesh