[gmx-users] metal ion go out of protein after md

[Tsjerk Wassenaar]

Nothing, except reading more about periodic boundary conditions. It
doesn't hurt though to understand that binding of ions such as Mn to
proteins involves charge transfer effects, that are hard to model
properly. This will cause a (further) deviation between your results
and reality. So be careful in drawing conclusions.

Cheers,

Tsjerk

On Wed, Mar 11, 2009 at 8:41 AM, Homa Azizian <hazizian at razi.tums.ac.ir> wrote:
> Hi
> MN in my active site participate in electrostatic intraction. I did not
> define any covalant bonds in topology file.
> What should I do in the case of Electrostatic intraction?
>
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> Tehran University of Medical Sciences
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
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