From: Norman Geist (
Date: Mon May 30 2016 - 00:51:46 CDT



If your solute is split by the periodic boundaries and are not connected by bonds, neither wrap –center com –centersel “your solute” nor pbc join can correctly work. But if there’s a single atom, which can represent the center of your solute so it will completely fit into the periodic cell, you can use that atom for –centersel


pbc wrap –all –compound res –center com –centersel „index 1234“



Norman Geist


Von: [] Im Auftrag von Chitrak Gupta
Gesendet: Freitag, 27. Mai 2016 19:48
An: Ajasja Ljubetič <>
Betreff: Re: vmd-l: Wrapping problem


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,



On Fri, May 27, 2016 at 12:10 PM, Ajasja Ljubetič < <> > 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
<> (link to movie)

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