How to recenter a waterbox with ions around my protein?

From: Maria Bykhovskaia (
Date: Thu Mar 28 2013 - 17:44:06 CDT

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 Bykhovskaia
Professor and Chair
Neuroscience Department
Universidad Central del Caribe
Bayamon, Puerto Rico

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