From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Jan 25 2010 - 08:55:05 CST

On Mon, Jan 25, 2010 at 8:50 AM, Mert Gür <gurmert_at_gmail.com> 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    akohlmey_at_gmail.com
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.