[gmx-users] salt bridge on protein surface

[David van der Spoel]

On Wed, 2004-11-24 at 07:03 +0000, Maarten Wolf wrote:
> Hello,
>  
> I am doing md simulations on a small peptide in water.
> These calculations result in a consistent salt bridge on the surface
> of the protein. 
> I find this strange, because I allways thought that salt-bridges on
> the surface are easily solvated, and thus broken.
> Is this assumption wrong? Or is this force field related? Or something
> else?  
The assumption is wrong in the sense the some saltbridges are stable and
others aren't. It may have to do with many things, e.g. a Lys has quite
a long hydrophobic that likes being packed. Can also be force field
related, or to the size of your box or the amount of counterions...
>  
> Thanks for any help in advance
> 
> 
> MvG Maarten
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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