From: M K (
Date: Tue Nov 11 2014 - 18:12:50 CST


I face a similar problem.
I simulate a polymer chain in water. I can select this chain using
"protein" selection. During the simulation, it moves and goes beyond the
boundaries of the box, and enters from the other side due to the periodic
I want to keep this polymer chain always in the center of the cubic box; a
good try is probably keeping the center of mass of the polymer chain in the
center of the box. I tried the following code and some other variations,
but they don't work; the chain is again split into parts when going beyond
the boundaries:

*pbc wrap -all -sel "protein" -center boundingbox -centersel "protein"*

Can someone please help? What is the problem with the code I'm using?

On Tue, Sep 30, 2014 at 12:14 AM, Josh Vermaas <>

> Hi Phan,
> You can use the PBCtools plugin (
> to rewrap your
> trajectory. If you just care about the hydrogen bonds between proteins,
> what you should be able to do is use something like this:
> pbc wrap -all -sel "protein" -center com -centersel "some atomselection
> text that only picks out one of the two protein copies"
> Then the selected protein will be near the center, and any of the atoms
> involved in hydrogen bonding should be inside the same unit cell. Read the
> documentation, and play around to see which combination of options you
> prefer.
> -Josh Vermaas
> On 09/29/2014 08:09 AM, Vy Phan wrote:
> Dear Vmd users,
> My systems for MD simulations included 2 protein, but after 50ns of
> trajectory, one protein go out side the water box (sometimes comeback). I
> knew why this phenomenon happened but when I do not know how to analyze the
> result.
> I have problem when I calculated hydrogen bonds between two protein.
> Because of the boundary condition, the result of hydrogen bonds is not
> right. How can I solve this problem?
> Thank a lot and best regards,
> Phan Vy