From: Mert Gür (
Date: Tue Jan 26 2010 - 15:31:45 CST

Dear Axel,
As you sugested I used the following command in order to center my cell
around the protein.

pbc wrap -center protein -first 0 -last 3000

Unfortunately it looks funny. There are long tube like bonds everywhere. I
wonder what is wrong with it? On the other hand when I plot the number of
hydrogen bonds among water and protein they seem to fluctuate around a value
which was not the case before (Which is good).
Can you please tell me if I am doing something wrong or are these long
tubelike structures normal?

On Mon, Jan 25, 2010 at 4:55 PM, Axel Kohlmeyer <> wrote:

> On Mon, Jan 25, 2010 at 8:50 AM, Mert Gür <> wrote:
> > Dear Leonardo,
> > I have read and tried the link you posted.
> > I think there have been an misunderstanding. Let's say 1/3th of my
> protein
> > is outside the water box (Not visually wrapped arround to the other side)
> > and the rest 2/3th is inside of it. So this 1/3th of my protein is
> wiggling
> > outside the box (Not on the other side). So there seem to be no water
> > molecules around it.
> so where is the problem?
> you use pbc wrap and give it the center of mass of the protein as a
> reference point for the center. then your protein should always be
> surrounded by water molecules. if not, you have used too few waters
> or made a mistake.
> cheers,
> axel.
> > Best,
> > Mert
> >
> --
> Dr. Axel Kohlmeyer
> Institute for Computational Molecular Science
> College of Science and Technology
> Temple University, Philadelphia PA, USA.