From: Josh Vermaas (
Date: Tue Nov 11 2014 - 18:23:25 CST

Yup, because you told it to center the box on the moving protein, and
only apply pbc corrections to the protein part, so PBCtools happily did
nothing. What I think you want to do (assuming you have no interest in
measuring the diffusion), is to move the entire system so that the
protein's center is at the origin, and then rewrap it (if desired) so
that the solvent molecules are on all sides of the polymer. The
rmsdtrajectory tool has a nice interface for this.

-Josh Vermaas

On 11/11/2014 06:12 PM, M K wrote:
> Hi,
> 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 nature.
> 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 <
> <>> wrote:
> 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