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