Re: crossing the border by protein/ion complex

From: Axel Kohlmeyer (
Date: Tue Feb 07 2012 - 17:33:08 CST

On Tue, Feb 7, 2012 at 6:16 PM, Maria Bykhovskaia
<> wrote:
> Hi,
> I am simulating a protein in a complex with several ions in a water box. The
> protein moves around the box, at some point crosses the border, and is
> wrapped around. However, the ions do not cross the border and are not
> wrapped, and this destroys the complex. In other simulations, one of the

this is only a visualization issue. due to periodic boundary conditions,
there are still the periodic copies of the atoms that are not (yet) wrapped.


> ions crosses the border, is wrapped around, and thus dissociates from the
> protein. Is there any way to treat the whole system as a complex in terms of
> crossing/ wrapping?
> Thanks a lot!
> Maria
> --
> Maria Bykhovskaia
> Professor and Chair
> Department of Neuroscience
> Universidad Central del Caribe
> Bayamon, Puerto Rico

Dr. Axel Kohlmeyer
College of Science and Technology
Temple University, Philadelphia PA, USA.

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