From: Axel Kohlmeyer (
Date: Thu Nov 15 2012 - 02:45:25 CST

On Thu, Nov 15, 2012 at 8:37 AM, Albert <> wrote:
> hello:
> I find that VMD doesn't interpret well for my system. The place of my
> protein becomes messy and I cannot analyze anything for MD results. Here is
> a screenshot for it:
> as we can see, the system is not in the PBC BOX, I try to use the command:

the location of the box as it is drawn
by pbctools is *completely* irrelevant.

what you may need is to wrap your solvent
around the solute. for this you can define
a selection that identifies the solute and
then use the -centersel flag to pbc wrap.

> pbc wrap -orthorhombic -shiftcenterrel {1 0 0}
> and the problem is still there.

you need to realize that a due to the translational invariance
of a periodic system, the location of the box itself does not
matter, only the relative positions of the solvent and the solute.


> I am just wondering how can I center my protein in the pbc box?
> thank you very much
> best
> Albert

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.