AW: crossing the border by protein/ion complex

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Wed Feb 08 2012 - 00:54:30 CST

Hi,

If you want to have better control on what is wrapped and how, you could
turn of the "wrapAll" command in your config and then wrap your system by
your needs in vmd with the pbc tools plugin. One have to think good about
what this wrapping stuff actually does. The Problem is that if you want to
wrap your protein, it will look "not so nice" because there will occur
overlong bonds. So you need to recenter the solvent around the box which can
be done with something like this:

pbc wrap -all -compound res -center com -centersel protein

But please read the VMD manual for that and double check whats going on.

Best wishes

Norman Geist.

> -----Ursprüngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von Axel Kohlmeyer
> Gesendet: Mittwoch, 8. Februar 2012 00:33
> An: Maria Bykhovskaia
> Cc: namd-l_at_ks.uiuc.edu
> Betreff: Re: namd-l: crossing the border by protein/ion complex
>
> On Tue, Feb 7, 2012 at 6:16 PM, Maria Bykhovskaia
> <mb.ucdelcaribe_at_gmail.com> 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.
>
> axel.
>
>
> > 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
> > http://maria.ucdelcaribe.com
> > http://neuro.ucdelcaribe.com
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com  http://goo.gl/1wk0
>
> College of Science and Technology
> Temple University, Philadelphia PA, USA.

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