[gmx-users] Counter ion and PME

[Tsjerk Wassenaar]

Hi David,

Yes, there has been a paper reporting on this point. No I haven't
analysed this with statistical rigour as you might have expected from
me. If you want the paper, I can dig it up for you.

Tsjerk

On 3/24/07, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> Tsjerk Wassenaar wrote:
> > Hi,
> >
> > Personally, I rather add ions up to physiological salt concentration,
> > in addition to counterions, which makes the equilibration quicker,
> > also accounts for the presence of both positive and negative charges
> > on the protein surface and, probably mainly due to the latter, has a
> > stabilizing effect on the proteins in simulation.
> >
> Not meaning to be cynical but where does this wisdom come from? It makes
> sense and most people will agree, but are you aware of any systematic tests?
>
>
> --
> 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://folding.bmc.uu.se
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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
F: +31-30-2537623