VMD-L Mailing List

From: Hitesh Patel (hiteshpatel379_at_gmail.com)
Date: Mon Nov 14 2011 - 10:17:12 CST

Hello,
pbc wrap -compound fragment -all
This command did not generate stretched bonds.. But, protein is going out
of the box.

I tried to keep the resid 35 at centre.. by
pbc wrap -compound fragment -centersel "resid 35" -all
But, It didn't work. It gave the same result as above command.

Thanks,

Regards,

Hitesh Patel

On Mon, Nov 14, 2011 at 4:57 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> 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.
>
> cheers,
> axel.
>
> > Thanks,
> > Regards,
> > Hitesh
>
>
>