Re: How to recenter a waterbox with ions around my protein?

From: Thomas Evangelidis (
Date: Fri Mar 29 2013 - 08:47:33 CDT

Try "pbc wrap -all -orthorhombic -compound fragment -center com -centersel
protein" in VMD or something equivalent.


On 29 March 2013 00:44, Maria Bykhovskaia <> wrote:

> I need to measure the distance between the protein and ions after
> prolonged MD. However, a part of the protein crossed the border of the cell
> (not wrapped around). I need to find out how close are certain ions to
> certain groups of the protein, but these protein groups moved out of the
> cell. Is there a way to recenter the water box with ions around the protein?
> Thank you,
> Maria
> --
> Maria Bykhovskaia
> Professor and Chair
> Neuroscience Department
> Universidad Central del Caribe
> Bayamon, Puerto Rico

Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
157 71 Athens


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