VMD-L Mailing List

From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Fri May 27 2016 - 12:47:36 CDT

Hi Ajasja,

Have you tried something like this?

pbc wrap -all -sel "water or ions" -compound res -center com -centersel
"protein"

This one works if:
1. All your chains are proteins
2. Only other things you have in your system apart from these chains come
under the category "water or ions".

You could modify this based on your needs, but you get the basic point.
Also, you could also change "-compound res" to "-compound fragment".

Hope this helps,
Chitrak.

On Fri, May 27, 2016 at 12:10 PM, Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com
> wrote:

> Dear All!
>
> I have run a simulation in NAMD using "wrapAll on". I'm simulating a
> complex of three chains.
> In one simulation (out of 14) I get large jumps, such as these
> <https://gfycat.com/CapitalHollowAmmonite> (link to movie)
> <https://gfycat.com/CapitalHollowAmmonite>:
>
> I have tried "pbc unwrap", "pbc wrap" and "pbc join", but Ihave yet to find
> the right combination of these command to correctly unwrap all three chains